What are Datasets?

Datasets are defined file collections, whose access is governed by a Data Access Committee (DAC).

Total number of Datasets: 3633
Displaying 1 - 3633

Dataset Accession Description Technologysort ascending Samples File Types
EGAD00010000600 Prostate Adenocarcinomas samples using 450K Illumina450K 80
EGAD00010000678 Tumor sample SNP arrays Illumina SNP array 11
EGAD00010000831 BLUEPRINT EpiMatch: harnessing epigenetics for hematopoietic stem cell transplantation Illumina Infinium HumanMethylation450 BeadChips 85
EGAD00010000752 German glioma case germline genotypes using Illumina HumanExome-12v1_A array Illumina HumanExome-12v1_A 899
EGAD00010000750 German glioma control germline genotypes using Illumina HumanExome-12v1_A array Illumina HumanExome-12v1_A 2,391
EGAD00010000758 French glioma case germline genotypes using Illumina HumanExome-12v1_A array Illumina HumanExome-12v1_A 906
EGAD00010000756 French glioma control germline genotypes using Illumina HumanExome-12v1_A array Illumina HumanExome-12v1_A 699
EGAD00010000754 UK glioma case germline genotypes using Illumina HumanExome-12v1_A array Illumina HumanExome-12v1_A 596
EGAD00001001646 Fastq files corresponding to RNA-Seq dataset for PTPN1 project (EGAS00001000554) Illumina Genome Analyzer II;, Illumina HiSeq 2000;, Illumina Genome Analyzer; 10 fastq
EGAD00010000850 BLUEPRINT DNA methylation profiles of monocytes, neutrophils and T cells from healthy donors Illumina 450K 525
EGAD00001002682 BLUEPRINT DNA methylation profiles of T cells in type 1 diabetes-discordant monozygotic twins Bisulfite-Seq 8 bam
EGAD00010000680 Tumor sample CGH arrays Agilent CGH array 4
EGAD00001003235 Raw exome sequence data(fastq) for the GATCI project unspecified;ILLUMINA 172
EGAD00001002693 Innate immune memory is the phenomenon whereby innate immune cells such as monocytes or macrophages undergo functional reprogramming after exposure to microbial components such as LPS. We apply an integrated epigenomic approach to characterize the molecular events involved in LPS-induced tolerance in a time dependent manner. ChIP-seq, RNA-seq, WGBS and ATAC-seq data were generated. This analysis identified epigenetic programs in tolerance and trained macrophages, and the potential transcription factors involved. Experimental set-up Time-course in vitro culture of human monocytes. Two innate immune memory states can be induced in culture through an initial exposure of primary human monocytes to either LPS or BG for 24 hours, followed by removal of stimulus and differentiation to macrophages for an additional 5 days. Cells were collected at baseline (day 0), 1 hour, 4 hour, 24 hour and 6 days. unspecified;, Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2000;, NextSeq 500; 71 fastq,bam
EGAD00001002453 ChIP-Seq data for 2 monocyte - RPMI_T=1hr sample(s). 4 run(s), 4 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 unspecified;, Illumina HiSeq 2000; 2 bam,fastq
EGAD00000000104 Gabriel samples from the Russian UFA cohort unknown 1
EGAD00000000098 Gabriel samples from the Swiss SALPADIA cohort unknown 1
EGAD00000000090 Gabriel samples from the Russian KMSU cohort unknown 1
EGAD00000000105 Gabriel samples from the multicenter occupational cohort unknown 1
EGAD00000000087 Gabriel samples from the multicenter GAIN cohort unknown 1
EGAD00000000092 Gabriel samples from the German MAGIS cohort unknown 1
EGAD00000000083 Gabriel samples from the French EGEA Cohort unknown 1
EGAD00000000088 Gabriel samples from the Karelia Allergy Study unknown 1
EGAD00000000076 Gabriel samples from the Australian Bussleton Cohort unknown 1
EGAD00000000095 Gabriel samples from the Dutch PIAMA cohort unknown 1
EGAD00000000093 Gabriel samples from the German MAGIS cohort unknown 1
EGAD00000000082 Gabriel samples from the French EGEA Cohort unknown 1
EGAD00000000102 Gabriel samples from the Russian TOMSK cohort unknown 1
EGAD00000000106 Gabriel samples from the multicenter occupational cohort unknown 1
EGAD00000000085 Gabriel samples from the German Gabriel Advanced Survey unknown 1
EGAD00000000108 Gabriel samples from the UK AUGOSA cohort unknown 1
EGAD00000000075 Gabriel samples from the Swedish BAMSE Cohort unknown 1
EGAD00000000107 Gabriel samples from the multicenter occupational cohort unknown 1
EGAD00000000091 Gabriel samples from the Russian KMSU cohort unknown 1
EGAD00000000101 Gabriel samples from the Russian TOMSK cohort unknown 1
EGAD00000000074 Gabriel samples from the Swedish BAMSE Cohort unknown 1
EGAD00000000103 Gabriel samples from the Russian UFA cohort unknown 1
EGAD00000000086 Gabriel samples from the multicenter GAIN cohort unknown 1
EGAD00000000077 Gabriel samples from the Australian Bussleton Cohort unknown 1
EGAD00000000097 Gabriel samples from the Swiss SALPADIA cohort unknown 1
EGAD00000000073 Gabriel samples from the 1958 British Birth Cohort unknown 1
EGAD00000000084 Gabriel samples from the German Gabriel Advanced Survey unknown 1
EGAD00000000089 Gabriel samples from the Karelia Allergy Study unknown 1
EGAD00000000094 Gabriel samples from the UK MRCA cohort unknown 1
EGAD00000000109 Gabriel samples from the UK SEVERE cohort unknown 1
EGAD00000000096 Gabriel samples from the Dutch PIAMA cohort unknown 1
EGAD00000000031 HLA genotyping of 1958 British Birth Cohort samples unknown 1
EGAD00010000622 SNP array data for gastric cancer cell lines unknown 30
EGAD00010000666 Purified plasma cells from tonsil of Healthy donor unknown 1
EGAD00010000668 Purified plasma cells from bone marrow of Monoclonal gammopathy of unknown significance patient unknown 1
EGAD00010000672 Purified plasma cells from bone marrow of Multiple myeloma patient unknown 1
EGAD00010000670 Purified plasma cells from bone marrow of Pooled healthy donors unknown 1
EGAD00000000121 Genotypes at MITF E318K variant Taqman and sequencing 2,488
EGAD00010000889 Gencode control samples using SNP6.0 SNP6.0 183
EGAD00010001216 Melanoma cell lines CNV by SNP6 SNP6 22
EGAD00010000874 Understanding Society Sequenom genotypes Sequenom 4,295
EGAD00010001420 Read counts determined using HTSeq-count for the BBMRI BIOS Freeze 2 RNAseq data RNAseq 3,560
EGAD00010001308 iOmics miRNA data via qPCR quantification patented mSMRT-qPCR miRNA assay (MIRXES) 351
EGAD00001003103 Cohort of 19 ADPKD patients characterized using long-read sequencing. The variant identification provided high sensitivity in identifying PKD1 pathogenic variants, with a diagnostic yield of 94.7%. This dataset includes all sequencing data (BAM files) of the 19 patients, in addition to their raw variants (unfiltered) obtained from the long-read sequencing as well as Sanger sequencing (VCF file). PacBio RS II;PACBIO_SMRT 19
EGAD00001001917 PacBio data for mesothelioma cell line NCI-H2595. PacBio RS II; 1 fastq
EGAD00010000466 Down syndrome CNV genotyping data NimbleGen 135K aCGH - NimbleScan 108
EGAD00001003280 NextSeq 550;ILLUMINA 16
EGAD00001003275 Targeted resequencing of samples was done with TruSeq custom amplicon low input kit (TSCA-LI, Illumina). The oligo capture probes were designed to include a prefix of 8 random nucleotides at the 5 end of each probe. The assay is designed such that each targeted locus is annealed with two probes, resulting in amplicons tagged with unique molecular identifiers (UMI) (22) of 16 bases. Raw FASTQ sequencing files were processed as following: (a) The first 8 bases were trimmed from each read and recorded with the corresponding base quality scores (BQ) in the attribute field. (b) Reads were aligned with BWA. (c) First round of PCR duplicate cleaning was performed with picard tools markDuplicates using the parameters BARCODE_TAG=BC TAGGING_POLICY=All REMOVE_DUPLICATES=true (d) Since in the previous step only duplicate reads with identical UMIs were removed, a second pass of filtering was done. Reads with identical mapping were considered unique only if their corresponding UMIs were different in at least 3 positions (i.e., UMI edit distance > 2). (e) Paired-end read pairs overlapping genomic positions were clipped to avoid overestimation of the sequencing coverage using bamUtils clipOverlap. NextSeq 550;ILLUMINA 74
EGAD00001002215 Low coverage whole genome sequencing plasma DNA from 50 male, 54 female non-cancer donors. For the analysis of nucleosomal positioning all data from the non-cancer controls were merged. Furthermore, two patients with metastasized breast cancer were sequenced on a NextSeq with higher depth. NextSeq 550;, Illumina MiSeq; 108
EGAD00001003788 Whole Exome Sequencing of 9 Colorectal Cancer (CRC) samples performed on Illumina HiSeq4000 consisting of aligned paired reads. RNAseq data sequenced on Illumina NextSeq500 consisting of FASTQ single reads from 3 CRC colon samples. A total of 12 samples from five patients (we matched normal tissue or pbmc and tumors) were sequenced on Illumina NextSeq500. NextSeq 500;ILLUMINA, Illumina HiSeq 4000;ILLUMINA 24
EGAD00001002917 ATAC-seq data for 2 sample(s) for germinal center B cell from tonsil, on Genome GRCh38. 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 2 bam,fastq
EGAD00001002708 ATAC-seq data for 7 sample(s) from tonsil, on Genome GRCh38. 7 run(s), 7 experiment(s), 7 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 7 bam,fastq
EGAD00001002710 ATAC-seq data for 4 sample(s) from bone marrow, on Genome GRCh38. 4 run(s), 4 experiment(s), 4 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 4 bam,fastq
EGAD00001002709 ATAC-seq data for 136 sample(s) from venous blood, on Genome GRCh38. 141 run(s), 139 experiment(s), 139 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 136 bam,fastq
EGAD00001002772 In this study we characterized genomic alterations in three bladder cancer patients with metastatic disease courses. Multiple regions were procured by laser microdissection or punctures from primary tumor, lymph node metastases and from distant metastases. Data provided here consist of 35 Bam files for WES (32 Tumors and 2 blood, 1 adjacent normal) NextSeq 500;ILLUMINA 35 bam
EGAD00001002899 ATAC-seq data for 1 sample(s) for monocyte RPMI_T=4hrs from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 1 bam,fastq
EGAD00001002909 ATAC-seq data for 1 sample(s) for monocyte RPMI_BG_T=24hrs from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 1 bam,fastq
EGAD00001002907 ATAC-seq data for 2 sample(s) for osteoclast from venous blood, on Genome GRCh38. 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 2 bam,fastq
EGAD00001002902 ATAC-seq data for 3 sample(s) for naive B cell from venous blood, on Genome GRCh38. 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 3 bam,fastq
EGAD00001002903 ATAC-seq data for 3 sample(s) for naive B cell from tonsil, on Genome GRCh38. 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 3 bam,fastq
EGAD00001002921 ATAC-seq data for 1 sample(s) for monocyte RPMI_T=24hrs from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 1 bam,fastq
EGAD00001002911 ATAC-seq data for 1 sample(s) for germinal center B cell from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 1 bam,fastq
EGAD00001002904 ATAC-seq data for 1 sample(s) for monocyte RPMI_BG_T=24hrs_RPMI_T=5days from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 1 bam,fastq
EGAD00001002918 ATAC-seq data for 5 sample(s) Mantle Cell Lymphoma from venous blood, on Genome GRCh38. 5 run(s), 5 experiment(s), 5 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 5 bam,fastq
EGAD00001002922 ATAC-seq data for 1 sample(s) for monocyte RPMI_LPS_T=4hrs from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 1 bam,fastq
EGAD00001002901 ATAC-seq data for 2 sample(s) for monocyte RPMI_LPS_T=24hrs_RPMI_T=5days from venous blood, on Genome GRCh38. 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 2 bam,fastq
EGAD00001002906 ATAC-seq data for 1 sample(s) for monocyte RPMI_BG_T=1hr from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 1 bam,fastq
EGAD00001002910 ATAC-seq data for 1 sample(s) for monocyte RPMI_BG_T=4hrs from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 1 bam,fastq
EGAD00001002915 ATAC-seq data for 1 sample(s) for monocyte RPMI_BG_T=24hrs_RPMI_T=5days_LPS_T=4hrs from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 1 bam,fastq
EGAD00001002916 ATAC-seq data for 106 sample(s) Chronic Lymphocytic Leukemia from venous blood, on Genome GRCh38. 111 run(s), 109 experiment(s), 109 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 106 bam,fastq
EGAD00001002900 ATAC-seq data for 1 sample(s) for monocyte RPMI_LPS_T=24hrs from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 1 bam,fastq
EGAD00001002919 ATAC-seq data for 1 sample(s) for monocyte RPMI_T=1hr from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 1 bam,fastq
EGAD00001002914 ATAC-seq data for 1 sample(s) for monocyte RPMI_T=6days from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 1 bam,fastq
EGAD00001002905 ATAC-seq data for 3 sample(s) for unswitched memory B cell from venous blood, on Genome GRCh38. 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 3 bam,fastq
EGAD00001002908 ATAC-seq data for 2 sample(s) for class switched memory B cell from venous blood, on Genome GRCh38. 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 2 bam,fastq
EGAD00001002912 ATAC-seq data for 2 sample(s) for plasma cell from tonsil, on Genome GRCh38. 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 2 bam,fastq
EGAD00001002913 ATAC-seq data for 1 sample(s) for monocyte RPMI_LPS_T=1hr from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 1 bam,fastq
EGAD00001002943 ChIPmentation data for 1 sample(s) for effector memory CD8-positive, alpha-beta T cell, terminally differentiated from venous blood, on Genome GRCh38. 5 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 1 bam,fastq
EGAD00001002939 ChIPmentation data for 3 sample(s) Burkitt Lymphoma from lymph node, on Genome GRCh38. 10 run(s), 8 experiment(s), 8 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 3 bam,fastq
EGAD00001002933 ChIPmentation data for 1 sample(s) for class switched memory B cell from venous blood, on Genome GRCh38. 2 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 1 bam,fastq
EGAD00001002936 ChIPmentation data for 5 sample(s) Acute Lymphocytic Leukemia for precursor B cell from venous blood, on Genome GRCh38. 7 run(s), 7 experiment(s), 7 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 5 bam,fastq
EGAD00001002928 ChIPmentation data for 7 sample(s) Acute Lymphocytic Leukemia for precursor B cell from bone marrow, on Genome GRCh38. 13 run(s), 13 experiment(s), 13 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 7 bam,fastq
EGAD00001002926 ChIPmentation data for 1 sample(s) for effector memory CD4-positive, alpha-beta T cell from venous blood, on Genome GRCh38. 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 1 bam,fastq
EGAD00001002944 ChIPmentation data for 2 sample(s) Activated B-Cell-Like Diffuse Large B-Cell Lymphoma from lymph node, on Genome GRCh38. 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 2 bam,fastq
EGAD00001002945 ChIPmentation data for 1 sample(s) for effector memory CD8-positive, alpha-beta T cell from venous blood, on Genome GRCh38. 2 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 1 bam,fastq
EGAD00001002927 ChIPmentation data for 1 sample(s) for central memory CD4-positive, alpha-beta T cell from venous blood, on Genome GRCh38. 5 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 1 bam,fastq
EGAD00001002938 ChIPmentation data for 2 sample(s) T-cell Acute Lymphocytic Leukemia from capillary blood, on Genome GRCh38. 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 2 bam,fastq
EGAD00001002931 ChIPmentation data for 3 sample(s) Lymphoma_Follicular from lymph node, on Genome GRCh38. 7 run(s), 6 experiment(s), 6 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 3 bam,fastq
EGAD00001002934 ChIPmentation data for 1 sample(s) for cytotoxic CD56-dim natural killer cell from venous blood, on Genome GRCh38. 2 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 1 bam,fastq
EGAD00001002924 ChIPmentation data for 2 sample(s) for central memory CD8-positive, alpha-beta T cell from venous blood, on Genome GRCh38. 11 run(s), 7 experiment(s), 7 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 2 bam,fastq
EGAD00001002930 ChIPmentation data for 1 sample(s) Acute Lymphocytic Leukemia from bone marrow, on Genome GRCh38. 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 1 bam,fastq
EGAD00001002929 ChIPmentation data for 1 sample(s) for CD38-negative naive B cell from cord blood, on Genome GRCh38. 5 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 1 bam,fastq
EGAD00001002942 ChIPmentation data for 2 sample(s) for regulatory T cell from venous blood, on Genome GRCh38. 13 run(s), 9 experiment(s), 9 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 2 bam,fastq
EGAD00001002940 ChIPmentation data for 1 sample(s) for conventional dendritic cell from cord blood, on Genome GRCh38. 4 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 1 bam,fastq
EGAD00001002925 ChIPmentation data for 1 sample(s) for immature conventional dendritic cell GM-CSF_IL4_T=6_days from venous blood, on Genome GRCh38. 2 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 1 bam,fastq
EGAD00001002946 ChIPmentation data for 2 sample(s) Germinal Center B-Cell-Like Diffuse Large B-Cell Lymphoma from lymph node, on Genome GRCh38. 6 run(s), 6 experiment(s), 6 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 2 bam,fastq
EGAD00001002941 ChIPmentation data for 1 sample(s) for mature conventional dendritic cell GM-CSF_IL4_T=6_days_R848_T=24hrs from venous blood, on Genome GRCh38. 2 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 1 bam,fastq
EGAD00001002935 ChIPmentation data for 2 sample(s) Acute Myeloid Leukemia for blast cell from bone marrow, on Genome GRCh38. 12 run(s), 6 experiment(s), 6 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 2 bam,fastq
EGAD00001002923 ChIPmentation data for 2 sample(s) for memory B cell from venous blood, on Genome GRCh38. 6 run(s), 4 experiment(s), 4 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 2 bam,fastq
EGAD00001002920 ATAC-seq data for 4 sample(s) Multiple Myeloma for plasma cell from bone marrow, on Genome GRCh38. 4 run(s), 4 experiment(s), 4 alignment(s). Part of BLUEPRINT (September 2016). NextSeq 500;ILLUMINA 4 bam,fastq
EGAD00001002691 RNAseq data for 10 patients: 10 tumors and 10 cell lines NextSeq 500;ILLUMINA 20
EGAD00001003148 Microfluidic direct library preparation (DLP) single-cell whole-genome BAM files for near-diploid immortalized lymphoblastoid cell line GM18507. NextSeq 500;ILLUMINA 192
EGAD00001002744 RNA sequencing data of human small intestinal macrophage subtypes NextSeq 500;ILLUMINA 15
EGAD00001002113 Mate pair whole genome sequencing data from 15 pediatric BCP ALL cases. Reference genome: hg19. Alignment: BWA 0.7.9a. NextSeq 500; 15 bam
EGAD00001003393 This dataset contains bam files for RNA-seq experiments for 6 neuroblastoma PDXs (Patient Derived Xenograft) and 3 pairs of neuroblastoma tumors at diagnosis and at relapse. NextSeq 500 (ILLUMINA), Illumina HiSeq 2500 (ILLUMINA), Illumina HiSeq 4000 (ILLUMINA) 12
EGAD00001003291 This dataset represents RNA-sequencing data from 278 primary colon cancers obtained from fresh-frozen tumor sections. RNA-sequencing was performed using TruSeq library preparation and samples were sequenced on Illumina NextSeq and HiSeq. The data are available as Illumina NextSeq and HiSeq fastq files (_R1.fastq and _R2.fastq for each tumor sample, 556 files in total). NextSeq 500 (ILLUMINA), Illumina HiSeq 2500 (ILLUMINA) 278
EGAD00010001276 Expression profiling by Nanostring cancer pathway Nanostring cancer pathway 30
EGAD00010001274 Expression profiling by Nanostring cancer immune Nanostring Cancer Immune 30
EGAD00010001074 Rare CNVs from schizophrenia cases and controls Mulitple CNV platforms 0
EGAD00001003387 MinION;OXFORD_NANOPORE 19
EGAD00001003382 MinION;OXFORD_NANOPORE 26
EGAD00001003511 BAM files with sequencing reads derived from Oxford Nanopore MinION whole genome sequencing of two DNA samples from lymphoblastoid cell lines from two patients with congenital disease. Samples were prepared using 1D and 2D library preps. MinION;OXFORD_NANOPORE 2
EGAD00010000983 MeDIP-seq RPM chromsome BED files for Peripheral Blood from EPITWIN Project (Columns 4-4353 represent samples) MeDIP-seq 4,350
EGAD00010001006 Proteomics LC-MS MS dataset Liquid chromatography–mass spectrometry 8
EGAD00000000054 NCI-H209 is an immortal cell line derived from a bone marrow metastasis of a patient with small cell lung cancer, taken before chemotherapy. The specimen showed histologically typical small cells with classic neuroendocrine features. NCI-BL209 is an EBV-transformed B-cell line derived from the same patient as the small cell lung cancer cell line, NCI-H209 Life Tech - Solid 1
EGAD00000000028 Aggregate results from a GWAS study on 3352 cases abd 3145 controls iSelect Beadchip 6,497
EGAD00001001010 Sequencing of colorectal tumors and normal tissue using Ion AmpliSeq Cancer Hotspot Panel V2 Ion Torrent Proton; 8 bam
EGAD00001002216 RNA-Seq on an Ion Torrent Proton of corresponding tumor material of two metastasized breast cancer patients (Breast7, Breast13). Ion Torrent Proton; 2
EGAD00001003131 The dataset consists of two main sample groups. 1) The inter-tumour sample group contains a total of 97 samples from 27 patients. Each patient has a single normal and primary sample as well as one or more metastases. All samples were sequenced using IonTorrent PGM and a custom colorectal cancer (CRC) panel. 2) The intra-tumour sample group contains a total of 68 samples from a single tumour as well as a normal tissue sample. All 68 samples were sequenced using IonTorrent PGM and a custom CRC panel. Shallow whole genome sequencing was additionally applied to 10 of the samples using Illumina HiSeq 4000. Ion Torrent PGM;ION_TORRENT, Illumina HiSeq 4000;ILLUMINA 193
EGAD00001000900 Multi-region Illumina whole-exome and/or whole-genome sequencing on tumor regions collected from early-stage NSCLC patients who underwent definitive surgical resection prior to receiving adjuvant therapy. Detected variants were validated on Ion AmpliSeqâ„¢ Custom Panel and/or Comprehensive Cancer Gene Panels. Patients covered by this dataset: L001, L002, L003, L004, L008 and L011. Ion Torrent PGM;, Illumina Genome Analyzer IIx; 28 bam,fastq
EGAD00001001044 Ion Torrent PGM; 2 bam
EGAD00001000889 NSCLC targeted. Ion Torrent PGM; 4 bam
EGAD00010001228 Primary and PDX SqCC samples using Infinium OmniExpress-24 Infinium_OmniExpress-24v1.0 24
EGAD00010000371 Case and control samples (Genotypes) Infinium_370k - GenomeStudio 170
EGAD00010001246 UK TGCT controls samples using theInfinium OncoArray-500K BeadChip Infinium OncoArray-500K BeadChip 7,422
EGAD00010001198 Case control samples using Infinium Omni2.5 Infinium Omni2.5M 274
EGAD00010000897 Infinium 450K in Rhabdomyosarcoma Infinium HumanMethylation450 BeadChip 53
EGAD00010001004 WTCCC1 project samples from 1958 British Birth Cohort Infinium 550K 1,504
EGAD00000000027 eQTL data for European newborns Ilumina HumanHap550-2v3_B-Beadstudio 176
EGAD00010000870 DNA methylation microarray Illumina_Infinium_HumanMethylation450 48
EGAD00010000562 Medulloblastoma DNA methylation Illumina_HumanMethylation450 115
EGAD00010001430 Gene expression analysis from primary human JMML samples using Illumina Human HT-12 v4 Illumina_HumanHT-12_V4 15
EGAD00010000869 RNA expression microarray Illumina_HumanHT-12v4 62
EGAD00010000492 Cases_Human660W-Quad_v1_A Illumina_Human660W-Quad_v1_A-Not supplied 4
EGAD00010000494 Controls_Human660W-Quad_v1_A Illumina_Human660W-Quad_v1_A-Not supplied 4
EGAD00010000506 WTCCC2 BO (Barretts oesophagus) samples Illumina_670k-Illuminus 1,991
EGAD00010000264 WTCCC2 project samples from Ischaemic Stroke Cohort Illumina_670k - Illuminus 4,205
EGAD00010000124 Psoriasis cases as part of WTCCC2 phase 2 Illumina_670k - Illuminus 2,622
EGAD00010000202 Case samples (Illumina_660K & Illumina_670K) Illumina_660K/Illumina_670K 1,478
EGAD00010001298 primary human ACC and normal samples using 450K Illumina_450K 110
EGAD00010001296 DNA methylation analysis from primary human JMML and normal blood samples using 450K Illumina_450K 0
EGAD00010000278 SCLC matched normal genotypes Illumina_2.5M 51
EGAD00010000276 SCLC tumor genotypes Illumina_2.5M 56
EGAD00010000274 Colon matched tumour samples Illumina_2.5M 74
EGAD00010000272 Colon tumour samples Illumina_2.5M 75
EGAD00010001064 tumor-based gene expression from breast cancer cases IlluminaHuman HT12 173
EGAD00010001063 blood-based gene expression from breast cancer cases IlluminaHuman AWG-6 and HT12 173
EGAD00010001062 blood-based gene expression from breast cancer cases and age-matched controls IlluminaHuman AWG-6 and HT12 455
EGAD00010000779 HipSci - Monogenic Diabetes - Genotyping Array - November 2014 Illumina, unknown 9
EGAD00010000300 Summary statistics from Haemgen RBC GWAS Illumina, Affymetrix, Perlegen 1
EGAD00010001192 Germline genotype data on 56,479 ovarian cancer cases and controls Illumina OncoArray 56,479
EGAD00010000260 PNET genotyping Illumina OmniQuad 2.5 - CNVpartition 77
EGAD00010000520 Healthy volunteer collection of European Ancestry Illumina OmniExpress v1.0-Illumina GenomeStudio 144
EGAD00010000417 Han Chinese samples using Illumina OMNIExpress (cases) Illumina OMNIExpress 62
EGAD00010000423 Han Chinese samples using Illumina OMNIExpress (controls) Illumina OMNIExpress 213
EGAD00010001200 Genotyping data from Indonesian sea nomad and surrounding populations Illumina Omni 5 105
EGAD00010000904 Genome-wide study of resistance to severe malaria in eleven worldwide populations:Kenya Illumina Omni 2.5M 3,865
EGAD00010000902 Genome-wide study of resistance to severe malaria in eleven worldwide populations:Gambia Illumina Omni 2.5M 5,594
EGAD00010001081 Summary statistics for Malaria Genomic Epidemiology Network, "A novel locus of resistance to severe malaria in a region of ancient balancing selection", Nature (2015) Illumina Omni 2.5M 11,657
EGAD00010000941 Gambian specimens without trachomatous scarring Illumina Omni 2.5 1,531
EGAD00010001422 1000G Phase 3 Imputed cases and controls from NSAID-induced PUD study Illumina Omni 2.5 676
EGAD00010001326 Papuan Genotyping Illumina Multi-EthnicGlobal_A1 380
EGAD00001003176 For each subject, genomic DNA from whole blood, circulating cell free DNA and tumor tissues (whenever possible) were performed targeting next generation sequencing on Illumina Miseq or Hiseq 4000 platforms. The sequencing results of whole blood were used to distinguish germline and somatic mutations. Specimens were collected from patients with different kinds of solid tumors, but most are lung cancer patients. Illumina MiSeq;ILLUMINA, Illumina HiSeq 4000;ILLUMINA 1,845
EGAD00001002678 The data set consists of low-pass whole genome sequence data of single CTCs, pools of CTCs and germline controls for a cohort of 31 SCLC patients at both baseline, and for 5 patients at relapse. In addition 9 CDX models and associated germline controls (where available) are included. Illumina MiSeq;ILLUMINA, Illumina HiSeq 2500;ILLUMINA, NextSeq 500;, NextSeq 500;ILLUMINA 319 fastq
EGAD00001003601 The dataset for Direct Detection of Early-Stage Cancers using Circulating Tumor DNA includes 602 bam files from next-generation sequencing on the Illumina HiSeq2500 or MiSeq. The samples analyzed include cancer cell lines as well as plasma and tissue specimens from healthy individuals and patients with cancer. Illumina MiSeq;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 550
EGAD00001002698 Recurrent breast cancer is almost universally fatal. We characterize 170 patients locally relapsed or distant metastatic cancers using massively parallel sequencing. We identify that the relapse-seeding clone disseminates late from the primary tumor. TP53 and AKT1 appear to be enriched in ER-positive cancers predisposed to relapse. Mutation acquisition continues at relapse as the same mutation signatures continue to operate and new signatures, such as that caused by radiotherapy appear de novo. In 49% of cases we identify drivers mutations private to the relapse and these are sampled from a wider range of cancer genes, including SWI-SNF complex and JAK-STAT signaling. Illumina MiSeq;ILLUMINA, Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 387 cram
EGAD00001002740 We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing. Illumina MiSeq;ILLUMINA, Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 164
EGAD00001003307 In this project we will use exome sequencing to identify somatic mutations in lesions from a patient with a germline mutation in the protection of telomeres 1 gene (POT1). This dataset contains all the data available for this study on 2017-04-27. Illumina MiSeq;ILLUMINA, Illumina HiSeq 2000;ILLUMINA 40
EGAD00001003145 Sensory neurons are nerve cells that are activated by sensory input such as heat, light and convey information to the brain. Although a key cell type in complex organisms, human sensory neurons are challenging to study because they are impossible to obtain from living donors. We have collaborated with the Neucentis Pharmaceutical Research Unit to differentiate sensory neuron like cells from human induced pluripotent stem cells derived as part of the Human Induced Pluripotent Stem Cells Initiative. We will sequence RNA from 100 IPS lines derived from healthy individuals and perform RNA-seq on the differentiated cells to identify noncoding variants that alter gene expression in human sensory neurons. Illumina MiSeq;ILLUMINA, Illumina HiSeq 2000;ILLUMINA 123
EGAD00001003119 TP53 targeted panel aligned reads consisting of BAM paired end reads from ovarian cancer tumor samples Data Access Committee Illumina MiSeq;ILLUMINA 76
EGAD00001003140 We analyzed the spectrum and clinical significance of MYC and BCL2 mutations in 347 DLBCL cases from population-based cohort of BC, Canada. Illumina MiSeq;ILLUMINA 347
EGAD00001003196 Amplicon-based fungal metagenomic sequencing for the identification of fungal species in brain tissue from Alzheimer's disease. The study consists in 14 samples, sequenced using Illumina's paired-end technology. Illumina MiSeq;ILLUMINA 14
EGAD00001003248 A BRAF V600E colorectal organoid which is sensitive to MAP kinase inhibition was mutagenised with the chemical mutagen ENU and then drug selected using a combination of Trametinib, Dabrafenib and Cetuximab. Single cell derived organoids were then manually picked and expanded in drug. Resistance was confirmed in a 14 day assay and DNA was collected. These then underwent targeted amplicon-based sequencing to confirm candidate resistance effectors from a screen in 2 2D BRAF V600E colorectal cell lines. Pools of resistant clones were also sequenced. Illumina MiSeq;ILLUMINA 36
EGAD00001003273 Low-coverage whole genome sequencing for the establishment of genomewide copy number alterations in pleura effusions and respective primary tumors Illumina MiSeq;ILLUMINA 20
EGAD00001003332 PCR and MiSeq validation for early embryonic substitution candidates from 400 Breast cancer patients This dataset contains all the data available for this study on 2017-05-11. Illumina MiSeq;ILLUMINA 4
EGAD00001003359 In this study, we present the results of a custom “pan-cardiomyopathy panel” in a molecular screening of 38 unrelated patients, 16 affected by DCM, 14 by HCM, and 8 by ARVC. The panel was designed using the Design Studio Tool (Illumina, San Diego, CA,USA). Coding regions and intron–exon boundaries of 115 genes, known to be associated with 7 DCM, HCM, and ARVC as well as channelopathies, were selected for targeted gene enrichment. For genes with multiple transcripts, all exons included in transcripts expressed in cardiac muscle were considered in the gene panel design. Total DNA was extracted from peripheral blood samples using the Wizard Genomic DNA Purification Kit (Promega, Mannheim, Germany) according to the manufacturer’s instructions, quantified, and qualitatively checked using NanoDrop 2000c (Thermo Fisher Scientific, Waltham, MA, USA). Custom targeted gene enrichment and DNA library preparation were performed using the Nextera Capture Custom Enrichment kit (Illumina) according to the manufacturer’s instructions. Targeted regions were sequenced using the Illumina MiSeq platform, generating approximately two millions of 150-bp paired-end reads for each sample (Q30 ≥90%). Illumina MiSeq;ILLUMINA 38
EGAD00001003400 We present targeted NGS panel data from 170 samples that were processed using the TruSightTM Cancer (TSC) panel (Illumina, San Diego, CA, USA), which targets 94 genes and 284 SNPs associated with a predisposition towards cancer. The samples are enriched for CNVs in the genes of interest. All CNVs have previously been assessed with MLPA and can therefore be considered as confirmed. Illumina MiSeq;ILLUMINA 170
EGAD00001003425 A EGFR mutant NSCLC cell line which is sensitive to AZD9291 inhibition was mutagenised with the chemical mutagen ENU and then drug selected using a AZD9291. Single cell derived colonies were then manually picked and expanded in drug. Resistance was confirmed in a 14 day assay and DNA was collected. These then underwent targeted amplicon-based sequencing to confirm candidate resistance effectors hypothesised from currently available literature. This dataset contains all the data available for this study on 2017-07-05. Illumina MiSeq;ILLUMINA 177
EGAD00001003579 Samples prepared using Safe-SeqS technology. All samples ran on an Illumina MiSeq instrument. Fastq files for read 1 and the index read present (R and I respectively). Illumina MiSeq;ILLUMINA 49
EGAD00001003453 16S sequencing of stool samples of LifeLines-DEEP, domain V4 Illumina MiSeq;ILLUMINA 1,010
EGAD00001003341 Sequence data from fungal infection isolated from neural tissue in ALS patients. Illumina MiSeq;ILLUMINA 34
EGAD00001003747 Optimisation of ex vivo Memory B cell Expansion/Differentiation for Interrogation of Rare Peripheral Memory B Cell Subset Responses 1) This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute please see http://www.sanger.ac.uk/datasharing/ This dataset contains all the data available for this study on 2017-09-13. Illumina MiSeq;ILLUMINA 38
EGAD00001003748 Sequencing of B-cell receptor repertoires in healthy individuals and patients with chronic lymphocytic leukemia. 1) This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute please see http://www.sanger.ac.uk/datasharing/ This dataset contains all the data available for this study on 2017-09-13. Illumina MiSeq;ILLUMINA 387
EGAD00001003436 Seven files of patients 3, 21, 29, 30, 31, 32 and 33 with WGS done on Illumina MiSeq with high coverage. For research purpose and authorised user only. Illumina MiSeq;ILLUMINA 7
EGAD00001003437 Fourteen files of patients 1, 2, 4, 6, 7, 8, 9, 12, 14, 16, 17, 18, 19 and 27 with WGS done on Illumina MiSeq with low coverage. For research purpose and authorised user only. Illumina MiSeq;ILLUMINA 14
EGAD00001001085 This dataset includes 2 pairs of tumour/normal whole genome sequence data as well as MEN1 gene targeted sequencing of an additional 87 specimens. Illumina MiSeq;, Illumina HiSeq 2500; 91 bam
EGAD00001001628 Illumina MiSeq;, Illumina HiSeq 2500; 142 bam
EGAD00001001674 Illumina MiSeq;, Illumina HiSeq 2500; 299 bam
EGAD00001002207 Our aim is to identify genes involved in resistance to anti-cancer therapies. In order to do this we have taken advantage of a lentiviral vector (LV)-based insertional mutagen to mutagenize cancer cell lines. LV-transduced cell lines were then treated with anti-cancer therapies and the emergence of resistant clones scored. DNA from pools of resistant clones was collected, subjected to custom capture by baits designed against the LV sequence, and then sequenced to identify the LV-genomic junction. We hope that the identification of recurrently targeted genes in resistant cell population will allow us to identify genes that mediate drug resistance. Illumina MiSeq;, Illumina HiSeq 2500; 71 cram
EGAD00001001662 Whole genome sequences of ACC primagrafts, Histone modification maps and transcription factor binding maps for ACC primagrafts and primary tumors. Processed ChIP-seq data is available on GEO under accession number GSE76465. Illumina MiSeq;, Illumina HiSeq 2000;, NextSeq 500;, Illumina HiSeq 2500; 58 bam,fastq
EGAD00001000605 CR products were obtained from each target loci using genomic DNA from human iPS cells. Subsequently, PCR products are pooled and subjected to Illumina library preparation. The library will be sequenced either by HiSeq or MiSeq. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina MiSeq;, Illumina HiSeq 2000; 10 bam
EGAD00001000798 In order to progress human induced pluripotent stem cells (hiPSCs) towards the clinic, several outstanding questions must be addressed. It is possible to reprogram different somatic cell types into hiPSCs but it is unclear whether some cell types carry through fewer mutations through reprogramming (either due to mutations present in the primary cells, or mutations accumulated during reprogramming). Through in depth analysis of hiPSCs generated from different somatic cells, it will be possible to assess the variation in genetic stability of different cell types. Illumina MiSeq;, Illumina HiSeq 2000; 28 bam
EGAD00001000822 Whole exome sequencing and miRNA-seq data of PPB. Illumina MiSeq;, Illumina HiSeq 2000; 18 bam
EGAD00001000974 High-grade serous ovarian cancer (HGSC) is characterized by poor outcome, often attributed to emergence of treatment-resistant sub-clones. We sought to measure the degree of genomic diversity within primary, untreated HGSC to examine the natural state of tumor evolution prior to therapy. We performed exome sequencing, copy number analysis, targeted amplicon deep sequencing and gene expression profiling on thirty-one spatially and temporally separated HGSC tumor specimens (six patients) including ovarian masses, distant metastases, and fallopian tube lesions. We found widespread intra-tumoral variation in mutation, copy number, and gene expression profiles, with key driver alterations in genes present in only a subset of samples (e.g. PIK3CA, CTNNB1, NF1). On average, only 51.5% of mutations were present in every sample of a given case (range: 10.2% to 91.4%), with TP53 as the only somatic mutation consistently present in all samples. Complex segmental aneuploidies, such as whole genome doubling, were present in a subset of samples from the same individual, with divergent copy number changes segregating independently of point mutation acquisition. Reconstruction of evolutionary histories showed one patient with mixed HGSC and endometrioid histology with common etiologic origin in the fallopian tube and subsequent selection of different driver mutations in the histologically distinct samples. In this patient, we observed mixed cell populations in the early fallopian tube lesion, indicating diversity arises at early stages of tumorigenesis. Our results reveal that HGSC exhibit highly individual evolutionary trajectories and diverse genomic tapestries prior to therapy, exposing an essential biological characteristic to inform future design of personalized therapeutic solutions and investigation of drug resistance mechanisms. Illumina MiSeq;, Illumina HiSeq 2000; 131 bam
EGAD00001001066 Dynamics of genomic clones in breast cancer patient xenografts at single cell resolution Illumina MiSeq;, Illumina HiSeq 2000; 188 bam
EGAD00001001332 Development of a method for separation and parallel sequencing of the genomes and transcriptomes of single cells. Illumina MiSeq;, HiSeq X Ten;, Illumina HiSeq 2500; 700 bam,cram
EGAD00001000364 We performed low coverage whole genome sequencing of plasma DNA from prostate cancer patients to establish copy number profiles on both a genome-wide and a gene-specific level. The data include plasma samples from prostate cacner patients (n=13), non-malignant controls (males, n=10 and females, n=9), plasma samples from pregnancies with aneuploid and euploid fetuses (n=4). Furthermore, we sequenced different tumor samples (n=6) of one patients and a serial dilution of HT29 in a background of normal DNA (n=9). Illumina MiSeq; 50 fastq
EGAD00001000396 We performed serial plasma-Seq analyses on a male who progressed from castration-sensitive to castration-resistant prostate cancer within 10 months following treatment with androgen-deprivation therapy. Illumina MiSeq; 2 fastq
EGAD00001001870 Deep sequencing of 151 cancer genes in 6 synchronous CRC of 3 patients Illumina MiSeq; 6 bam
EGAD00001000365 In this study we analysed patients with metastatic prostate cancer to scan their tumor genomes noninvasively in plasma DNA. We enriched 1.3 Mbp of seven plasma DNAs (4 CRPC cases: CRPC1-3 and CRPC5; 3 CSPC cases: CSPC1-2 and CSPC4) including exonic sequences of 55 cancer genes and 38 introns of 18 genes, where fusion breakpoints have been described using Sure Select Custom DNA Kit. Illumina MiSeq; 7 fastq
EGAD00001000357 PCR products were obtained from each target loci using genomic DNA from human iPS cells. Subsequently, PCR products are pooled and subjected to Illumina library preparation. The library will be sequenced by MiSeq. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina MiSeq; 4 bam
EGAD00001000392 Agilent whole exome hybridisation capture was performed on genomic DNA derived from Chondrosarcoma cancer and matched normal DNA from the same patients. Next Generation sequencing performed on the resulting exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes. Now we aim to re find and validate the findings of those exome libraries using bespoke pulldown methods and sequencing the products. Illumina MiSeq; 60 bam
EGAD00001000606 Background Massively parallel sequencing technology has transformed cancer genomics. It is now feasible, in a clinically relevant time-frame, for a clinically manageable cost, to screen DNA from patient tumours for mutations essentially genome-wide. The challenge for personalised medicine will be to increase the sample size to thousands or tens of thousands of well-characterised cases in order to attain sufficient statistical power to stratify patients accurately across the complexity and genomic heterogeneity expected for most of the common tumour types. Currently, whole genome sequencing on this scale is not feasible, and targeted sequencing of relevant portions of the genome will be required. Pilot data We have developed protocols for large-scale, multiplexed sequencing of 100-200 genes in thousands of samples. Essentially, using robotic technology, genomic DNA from the cancer specimen is processed into sequencing libraries with unique DNA barcodes, thereby allowing sequencing reads to be attributed to the sample they derive from. Currently, these sequencing libraries can be generated in a 96-well format using fully automated protocols, and we are exploring methods to expand this to a 384-well format. The sequencing libraries are pooled and hybridized to custom sets of RNA baits representing the genomic regions of interest. Sequencing of the pulled-down libraries is done in pools of 48-96 samples per lane of an Illumina Hi-Seq. This protocol is already implemented at the Sanger Institute. We have published proof that somatic mutations in novel cancer genes can be identified from exome-wide sequencing. In unpublished pilot data, we have established the feasibility of robotic library production, custom pull-down, and multiplexed sequencing of barcoded libraries for 100 known myeloid cancer genes across 760 myelodysplasia samples. Highlights of the data thus far analysed reveal that the coverage is remarkably even between samples; when 96 samples are run, average coverage per lane of sequencing is ~250, with 90-95% of targeted exons covered by >25 reads; known mutations can be discovered in the data set; and the protocol is amenable to whole genome amplified DNA. The bioinformatic algorithms for identification of substitutions and indels in pull-down data are well-established; we have pilot data proving that copy number changes, LOH and genomic rearrangements in specific regions of interest can also be identified by tiling of baits across the relevant loci. Proposal We propose to apply this methodology to 10000 samples from patients with AML enrolled in clinical trials over the last 10-20 years. Oncogenic point mutations and potentially genomic rearrangements will be identified, and linked to clinical outcome data, with a view to undertaking the following sorts of analyses: ? Identification of co-occurrence, mutual exclusivity and clusters of driver mutations. ? Correlation of prognosis with driver mutations and potentially gene-gene interactions ? Exploration of genomic markers of drug response Ultimately, we would like to be in a position to release the mutation data together with matched clinical outcome data to genuine medical researchers via a controlled access approach, possibly within the COSMIC framework (www.sanger.ac.uk/genetics/CGP/cosmic/). The vision here is to generate a portal whereby a clinician faced with an AML patient and his / her mutational profile can obtain a ?personalised? prediction of outcome, together with a fair assessment of the uncertainty of the estimate. With a sufficient sample size, there would also be the potential to develop decision support algorithms for therapeutic choices based on such data. Illumina MiSeq; 38 bam
EGAD00001000607 PCR products were obtained from each target loci using genomic DNA from human iPS cells. Subsequently, PCR products are pooled and subjected to Illumina library preparation. The library will be sequenced either by HiSeq or MiSeq. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina MiSeq; 2 bam
EGAD00001000608 PCR products were obtained from each target loci using genomic DNA from human iPS cells. Subsequently, PCR products are pooled and subjected to Illumina library preparation. The library will be sequenced either by HiSeq or MiSeq. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina MiSeq; 60 bam
EGAD00001000621 We propose to definitively characterise the somatic genetics of Prostate cancer through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing. This study will aim to validate the findings of the whole genome study by re-sequencing regions of interest using a bespoke pulldown bait. See ICGC website for more information: http://icgc.org/icgc/cgp/70/508/71331 Illumina MiSeq; 18 bam
EGAD00001001313 We enriched a panel of cancer associated genes using the Custom Sure Select Target Enrichment Kit. Identified mutations were validated with deep sequencing in order to assess mutated allele frequencies more accurately. Illumina MiSeq; 10 fastq
EGAD00001000688 In this study we performed ultra deep sequencing of genes associated with anti-EGFR resistance, such as KRAS, BRAF, PIK3CA, and EGFR in 17 plasma-DNA samples from a total of 10 patients treated with anti-EGFR therapy. Illumina MiSeq; 25 bam
EGAD00001000748 In this study we performed whole genome sequencing of plasma DNA (plasma-Seq) of 19 plasma-DNA samples from a total of 10 patients treated with anti-EGFR therapy. We demonstrated that development of resistance to anti-EGFR therapies is frequently associated with focal amplifications of KRAS, MET, and ERBB2. We also showed that focal KRAS amplifications can be acquired in tumor genomes of patients under cytotoxic chemotherapy. Furthermore, we provide evidence that specific chromosomal polysomies, such as overrepresentations of 12p and 7p, harboring KRAS and EGFR, respectively, determine responsiveness to anti-EGFR therapy. Illumina MiSeq; 19 fastq
EGAD00001002225 This study involves targeted sequencing of samples from myeloid malignancies at different timepoints to assess clonal evolution of malignancy a. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina MiSeq; 147 cram
EGAD00001000786 We are interested in the contribution mutations in the Shelterin complex protein POT1 may have to the development of melanoma. We have identified a patient who carries a splice site mutation in POT1 and as part of our analysis of this gene we aim to sequence the transcriptome of this patient to see how this mutation influences splicing. RNA has been obtained from lymphocytes collected from the patient. Illumina MiSeq; 1 cram
EGAD00001000445 We recently worked-up a pulldown protocol for studying 21 genes recurrently mutated in AML (Study1770). Our manuscript is currently under revision and to address the reviewers' comments we need to validate some mutations by re-sequencing. In this add-on study we will be using PCR followed by MiSeq for this purpose. Illumina MiSeq; 9 bam
EGAD00001000827 n order to progress human induced pluripotent stem cells (hiPSCs) towards the clinic, several outstanding questions must be addressed. It is possible to reprogram different somatic cell types into hiPSCs and from studies in the mouse, it appears that an epigenetic memory of the starting cell type is carried over to hiPSCs. However a comprehensive comparative study of the characteristics of these hiPSCs has been missing from the literature. Importantly studies which aimed to address these aspects of hiPSCs have used cells from different patients. In order to avoid this important confounding variable and to keep the genetic background constant, tissue samples were procured from the patients and reprogrammed to iPS cells. The methylation status of these iPS cells will be compared. Protocol: Primary cell cultures were generated and reprogrammed to iPS cells. DNA was extracted and immunoprecipitated using anti-methyl cytosine and anti-hydroxymethyl cytosine antibodies. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina MiSeq; 4 bam,cram
EGAD00001000631 PCR products were obtained from each target loci using genomic DNA from human iPS cells. Subsequently, PCR products are pooled and subjected to Illumina library preparation. The library will be sequenced either by HiSeq or MiSeq. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina MiSeq; 4 bam
EGAD00001000848 To evaluate the presence of mutations in frequently mutated genes in MPN by performing targeted resequencing of a selected gene panel comprising of 111 genes across 40 samples with MPN. Illumina MiSeq; 48 cram
EGAD00001000819 We are aiming to investigate repair of a double strand break (DSB) within the genome in the presence and absence of the BLOOM protein. Zinc Finger Nucleases introduce DSBs at specified loci within the genome. Using sequencing we will assess the size of the deletion following repair. Protocol 1. Transfect normal and BLOOM deficient human iPS cells with ZFNs, using AMXA 2. Harvest cells after 5 days 3. Perform column extraction of DNA 4. PCR-amplify the ZFN region 5. Sequence and analyse repair of the DSB This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina MiSeq; 6 bam
EGAD00001001314 Sequence data from L1-amplicon libraries prepared from plasma-DNA from a set of 24 female controls and 18 male controls without malignant disease and samples from patients breast (n= 28) and prostate cancer patients (n=61). Illumina MiSeq; 125 fastq
EGAD00001001242 Pilot study to set up sequencing protocols for targeted pulldown methylation profiling Illumina MiSeq; 2 cram
EGAD00001000763 We used targeted deep sequencing to accurately establish the allele frequencies of the mutations identified by exome sequencing Illumina MiSeq; 23 bam
EGAD00001000761 In order to establish copy number profiles from the various samples we prepared libraries and subjected them to whole-genome sequencing at a shallow sequencing depth (0.1x) Illumina MiSeq; 14 fastq
EGAD00001001850 Genomic DNA from Swedish control individuals was pooled. Then the genomic sequence of brain expressed miRNA genes was determined in the pools. Illumina MiSeq; 149 fastq
EGAD00001001852 Genomic DNA from Belgian control individuals was pooled. Then the genomic sequence of brain expressed miRNA genes was determined in the pools. Illumina MiSeq; 39 fastq
EGAD00001001849 The genomic sequence of brain expressed miRNA genes was sequenced in Swedish schizophrenia patients Illumina MiSeq; 186 fastq
EGAD00001001851 The genomic sequence of brain expressed miRNA genes was sequenced in Belgian epilepsy patients. Illumina MiSeq; 163 fastq
EGAD00001001028 DNA belonging to 16 tumour/normal samples were treated with bisulfite, then up to 5 different bisulfite PCRs were performed in each one of the samples. Amplicons form the same sample were pooled and submitted to sequencing on a MiSeq platform. Illumina MiSeq; 18 cram
EGAD00001002194 This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ We performed exome sequencing on serial samples from a patient with CMML who progressed to AML. The exome sequencing suggests that NPM1, TET2 and DNMT3a mutations were present in the dominant clone in the CMML sample and that NRAS is a new subclonal mutation in the AML sample. Diagnostic data shows the presence of a FLT3-ITD mutation in the AML sample, which is likely to have driven progression. Here we are performing re-sequencing of the putative driver and some passenger mutations which appear to be in the same clone to validate these mutations and to verify the relative quantification of these abnormalities . Illumina MiSeq; 10 cram
EGAD00001002196 Our lab is currently using macrophages as a model system for understanding how genetic variation modulates the response to external environmental stimulus. We want to extend this beyond regular polyadenylated RNA to small RNAs such as miRNAs. This project would cover the costs of a pilot to study miRNA response to LPS stimulus, and will be performed as part of a rotation project in the lab. We will require a small number of miRNA libraries and a single lane of MiSeq Illumina MiSeq; 6 cram
EGAD00001000980 This study involves a forward genetic screen to identify common insertion sites in drug resistant clones. We will be utilising piggybac transposon systems in order to generate multiple drug resistant clones in a range of human cancer cell lines. Illumina MiSeq; 144 bam,cram
EGAD00001001062 Patient (who has had multiple malignancies) has previously been found to harbour a pathogenic p53 variant which is probably mosaic. This finding is based on exome sequencing performed elsewhere. In this study we will resequence the locus in question to ascertain whether the variant is indeed mosaic. Illumina MiSeq; 4 cram
EGAD00001001064 Extension of angiosarcoma whole genome sequencing study Illumina MiSeq; 4 cram
EGAD00001001061 This experiment is to inform us of the validity of using pre-made library material to perform a bespoke pulldown experiment to validate the mutations found between the whole genome sequencing of the DNA from the same individuals cancer and normal material. This is to identify the valid and informative mutations in cancer genomes. Illumina MiSeq; 4 bam
EGAD00001001072 Illumina MiSeq; 5 fastq
EGAD00001001451 JMML targeted sequencing of candidate genes Illumina MiSeq; 75 bam
EGAD00001001930 Cancer genes can affect ribosomal RNA processing and this can underlie their essentiality to cells, making them cell-essential in the same way as ribosomal genes themselves. We want to confirm this, in order to understand the results of our CRISPR drop-out screens. NOTE FROM BESPOKE TEAM: Run a single read 1 (forward read) of 30 bases, then an index 1 read as normal. This would fit a 50cycle kit Illumina MiSeq; 6 cram
EGAD00001001104 MMP-seq tumor samples, UDG treated (FASTQ) Illumina MiSeq; 16 fastq
EGAD00001001319 The aim of this study is to ascertain whether leukaemic mutations exist within the blood of people with otherwise normal haematopoeisis. To satisfy this aim we plan to look for 7 known leukaemic mutations in the whole blood DNA of a large cohort of blood donors who have normal haematopoesis. Genomic regions around mutational sites have been amplified using a 2 step PCR process which involves barcoding of individual patients Illumina MiSeq; 5,817 cram
EGAD00001001317 This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina MiSeq; 12 cram
EGAD00001001320 This is a study to test ATAC-seq protocols. CD4+ and CD8+ cells have been obtained from three different anatomical compartments. We aim to assay open-chromatin regions across these cells and perform comparative analyses. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina MiSeq; 138 cram
EGAD00001001421 Clinical Implications of Genomic Alterations in the Tumour and Circulation of Pancreatic Cancer Patients Illumina MiSeq; 125 fastq
EGAD00001001439 Mammary cell samples from donors 28/32/33. Contains 12 MiSeq sequence files and 12 alignment files derived from HiSeq runs. Illumina MiSeq; 12 fastq,bam
EGAD00001001445 Deep sequencing of melanoma for driver mutations Illumina MiSeq; 3 cram
EGAD00001001448 Testing the feasibility of genome-scale sequencing in routinely collected formalin-fixed paraffin-embedded (FFPE) cancer specimens versus matched fresh-frozen samples using targeted pulldown capture prior to Illumina sequencing. Illumina MiSeq; 11 bam
EGAD00001001449 PCR products were obtained from each target loci using genomic DNA from human iPS cells. Subsequently, PCR products are pooled and subjected to Illumina library preparation. The library will be sequenced either by HiSeq or MiSeq. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina MiSeq; 6 bam
EGAD00001001600 PCR and MiSeq validation for early embryonic substitution candidates from 400 Breast cancer patients. This dataset contains all the data available for this study on 2015-09-03. Illumina MiSeq; 2 cram
EGAD00001001631 Illumina MiSeq; 334 fastq
EGAD00001001667 Data from the paper Context-specific Effects of TGFβ/SMAD3 in Cancer Are Modulated by the Epigenome. Tufegdzic et al, Cell Reports 2015 Illumina MiSeq; 12 bam
EGAD00001001935 Cancer amplicon reads consisting of BAM paired end reads from primary multiple myeloma samples. Illumina MiSeq; 88 bam
EGAD00001001983 Immunoglobulin heavy chain gene high throughput sequencing of paediatric acute lymphoblastic leukaemia samples, for the purpose of MRD on the Illumina MiSeq platform. This dataset contains summary fastq files and raw bcl files from the MiSeq for this study. In the study we identify errors associated with multiplexing that could potentially impact on the accuracy of MRD analysis. We optimise a strategy combining high purity, sequence-optimised oligonucleotides, dual-indexing and an error-aware demultiplexing approach to minimise errors and maximise sensitivity. Illumina MiSeq; 491 fastq
EGAD00001001937 Targeted sequencing of 48 amplicons in TP53, PTEN, EGFR, PIK3CA, KRAS and BRAF genes was performed as described previously [Forshew, STM 2012]. All libraries were pooled and quantify using DNA 1000 kit on Agilent 2100 Bioanalyzer and KAPA SYBR FAST ABI Prism qPCR Kit (KAPA Biosystems) on 7900HT Fast Real-Time PCR System (Applied Biosystems) according to the supplier's recommendations. Reads were aligned using bwa-mem v0.7.12-r1039 to the 1000 genomes version of human genome build GRCh37, retaining duplicate reads. Illumina MiSeq; 66 bam
EGAD00001002108 Exome and targeted amplicon sequencing data for tumor, germline and plasma samples from a patient with metastatic breast cancer. Illumina MiSeq; 30 bam
EGAD00001002150 Low coverage whole genome sequencing for the identification of somatic copy number alterations (SCNA) and focal amplification mapping of corresponding tumor material Illumina MiSeq; 8 fastq
EGAD00001002118 Raw data (fastq files) from targeted resequencing of AML patients at relapse Illumina MiSeq; 24 fastq
EGAD00001002217 Merged file of low-coverage WGS from 179 plasma DNA samples from non-cancer controls and cancer patients for assessment of size distribution of plasma nuclear DNA fragments. Illumina MiSeq; 1 bam
EGAD00001002189 paired-end BAM files of the sequencing analysis of the mtDNA polymerase gamma (POLG) gene in the MS-affected co-twins Illumina MiSeq; 54 bam
EGAD00001002190 Single-end BAM files of the targeted deep sequencing analysis of several mtDNA candidate regions in blood and buccal-derived DNA of the corresponding twin pairs. Illumina MiSeq; 140 bam
EGAD00001002149 Low coverage whole genome sequencing for the identification of somatic copy number alterations (SCNA) and focal amplification mapping in plasma DNA of prostate cancer patients Illumina MiSeq; 95 fastq
EGAD00001002117 Raw data (fastq files) from targeted resequencing of AML patients at diagnosis Illumina MiSeq; 68 fastq
EGAD00001002252 This data set contains next generation sequencing (NGS) data of two serial tumor samples (primary and a metastasis) from a patient with colorectal cancer showing an ERBB2 c.2264T>C (p.Leu755Ser). NGS was performed using the Illumina TruSeq Amplicon Cancer Panel (TSACP, Illumina) covering 212 amplicons in 48 cancer associated genes on the Illumina MiSeq sequencing platform. The dataset contains two BAM files. Illumina MiSeq; 2 bam
EGAD00001002254 Single-end sequencing data (trimmed to 60bp) of 104 plasma samples from donors without tumors (male=50; female=54) were merged and used to establish coverage profiles around the TSS and to establish a gene expression prediction algorithm. Dataset includes merged alignements of low coverage whole genome sequencing from plasma DNA from 50 male, 54 female non-cancer donors. Furthermore, 2 patients with metastasized breast cancer were sequenced on a NextSeq with higher depth. Illumina MiSeq; 3 bam
EGAD00001001942 We performed target re-sequencing for 1.29 Mb interval of chromosome 9 (chr9:21299764–22590271, hg19). NimbleGen SeqCap EZ choice system was used as a target enrichment method (Roche Diagnostics). A DNA probe set complementary to the target region was designed by NimbleDesign. The libraries were sequenced on the Illumina MiSeq platform with 2×150-bp paired-end module (Illumina). Fastq files for 48 Japanese patients with endometriosis are deposited. Illumina MiSeq; 48
EGAD00001001936 Firs 1106 16S rDNA data for the Flemish Gut Flora Project Illumina MiSeq; 1,061
EGAD00010000865 MBDSEQ Illumina MBD-Sequencing 16
EGAD00010001285 Genotyping of knee osteoarthritis patients who have undergone total joint replacement Illumina InfiniumCoreExome-24v1-1_A 17
EGAD00010001289 Resolving the Genetic Architecture of Aseptic Loosening After Total Hip Replacement Illumina InfiniumCoreExome-24v1-1_A 2,880
EGAD00010001292 Genotyping of hip osteoarthritis patients who have undergone total joint replacement Illumina InfiniumCoreExome-24v1-1_A 9
EGAD00010001323 Medulloblastoma methylation profiling Illumina Infinium HumanMethylation450 BeadChip 911
EGAD00010001319 Medulloblastoma methylation profiling Illumina Infinium HumanMethylation450 BeadChip 345
EGAD00010000482 ccRCC case samples using methylation array Illumina Infinium HumanMethylation 450K - GenomeStudio 1
EGAD00010001243 UK TGCT control samples using the Infinium 1.2M array Illumina Infinium 1.2M array 4,946
EGAD00000000058 Aggregate results from 22 Carbamazepine-induced hypersensitivity syndrome patients and 2691 UK National Blood Service (NBS) control samples Illumina Infinium 1.2M 2,713
EGAD00010000928 WTCCC3_Primary Biliary Cirrhosis Replication Post-QC Illumina ImmunoChip 2,861
EGAD00010000929 WTCCC3_Primary Biliary Cirrhosis Replication Illumina ImmunoChip 2,981
EGAD00010000250 NBS control samples Illumina ImmunoBeadChip - Illuminus, GenoSNP 3,030
EGAD00010000246 Coeliac disease cases and control samples. (1958BC samples excluded) Illumina ImmunoBeadChip - Illuminus, GenoSNP 10,758
EGAD00010000248 1958BC control samples Illumina ImmunoBeadChip - Illuminus, GenoSNP 6,812
EGAD00010001412 Blood transcriptome from women participating in the Norwegian Women and Cancer study (NOWAC) Illumina HumanWG-6 version 3 or Illumina HumanHT-12 expression bead chip, combined on identical nucleotide universal identifier 920
EGAD00010001400 Difference in gene expression values between case and control, log2 values. Blood transcriptome from women participating in the Norwegian Women and Cancer study (NOWAC) Post-genome Cohort taken up to eight years before brest cancer diagnosis. Illumina HumanWG-6 version 3 or Illumina HumanHT-12 expression bead chip, combined on identical nucleotide universal identifiers. Illumina HumanWG-6 467
EGAD00010001179 Tissue samples using Illumina HumanOmniExpress-FFPE-12 v1.0 BeadChip Illumina HumanOmniExpress-FFPE-12 v1.0 BeadChip 22
EGAD00010000952 Where Are You From? samples types at 517K SNP loci Illumina HumanOmniExpress-24 BeadChip 598
EGAD00010001212 Genetic studies of pregnancy-related cardiometabolic disorders in Central Asian, Northern European, and Colombian populations Illumina HumanOmniExpress-12v1_J 1,207
EGAD00010000560 SNP array of 7 HCCs and matched background liver in children with bile salt export pump deficiency Illumina HumanOmniExpress-12 v1. 14
EGAD00010001209 Genome-wide SNP genotyping data for 1,235 western Africans by Illumina HumanOmniExpress-12 array, used in the EGAS00001002078 study Illumina HumanOmniExpress-12 1,235
EGAD00010001131 The 100 European-descent (EUB) and 100 African-descent (AFB) Belgians studied were genotyped for a total of 4,301,332 SNPs on the Illumina HumanOmni5-Quad BeadChips. Whole-exome sequencing was carried out for the same 200 individuals with the Nextera Rapid Capture Expanded Exome kit, on the Illumina HiSeq 2000 platform, with 100-bp paired-end reads. This kit delivers 62 Mb of genomic content per individual, including exons, untranslated regions (UTR), and microRNAs. Omni5 and exome datasets were merged, yielding a concordance rate between platforms of 99.93%. Illumina HumanOmni5-Quad and exome sequencing 200
EGAD00010001102 Genotype data from Chad, Lebanon, and Yemen Illumina HumanOmni2.5-8 v1.2 A 126
EGAD00010001101 Genotype data from Chad, Lebanon, and Yemen Illumina HumanOmni2.5-8 v1.1 B 20
EGAD00010001103 Genotype data from Chad, Lebanon, and Yemen Illumina HumanOmni2.5-8 v1.1 B 238
EGAD00010000965 Array data from 4778 individuals from general population of rural Uganda Illumina HumanOmni2.5-8 BeadChip 4,778
EGAD00010001053 APCDR AGV Project: Array data from 100 Banyarwanda. Raw data, intensity files and post-QC Plink files. Illumina HumanOmni2.5-4v1_B and HumanOmni2-5_8v1_A 100
EGAD00010001058 APCDR AGV Project: Array data from 100 Ga-Adangbe. Raw data, intensity files and post-QC Plink files. Illumina HumanOmni2.5-4v1_B and HumanOmni2-5_8v1_A 100
EGAD00010001055 APCDR AGV Project: Array data from 100 Baganda. Raw data, intensity files and post-QC Plink files. Illumina HumanOmni2.5-4v1_B and HumanOmni2-5_8v1_A 100
EGAD00010001056 APCDR AGV Project: Array data from 100 Zulu. Raw data, intensity files and post-QC Plink files. Illumina HumanOmni2.5-4v1_B and HumanOmni2-5_8v1_A 100
EGAD00010001049 APCDR AGV Project: Array data from 99 Kikuyu. Raw data, intensity files and post-QC Plink files. Illumina HumanOmni2.5-4v1_B 99
EGAD00010001045 APCDR AGV Project: Array data from 99 Igbo. Raw data, intensity files and post-QC Plink files. Illumina HumanOmni2.5-4v1_B 99
EGAD00010001052 APCDR AGV Project: Array data from 100 Kalenjin. Raw data, intensity files and post-QC Plink files. Illumina HumanOmni2.5-4v1_B 100
EGAD00010000468 Uveal melanoma matched Tumour and blood samples Illumina HumanOmni2.5 24
EGAD00010000943 Sahel population study using 2.5M Illumina HumanOmni2.5 161
EGAD00010001046 APCDR AGV Project: Array data from 86 Sotho. Raw data, intensity files and post-QC Plink files. Illumina HumanOmni2-5_8v1_A 86
EGAD00010001057 APCDR AGV Project: Array data from 88 Mandinka. Raw data, intensity files and post-QC Plink files. Illumina HumanOmni2-5_8v1_A 88
EGAD00010001054 APCDR AGV Project: Array data from 74 Fula Illumina HumanOmni2-5_8v1_A 74
EGAD00010001051 APCDR AGV Project: Array data from 97 Barundi. Raw data, intensity files and post-QC Plink files. Illumina HumanOmni2-5_8v1_A 97
EGAD00010001050 APCDR AGV Project: Array data from 78 Wolof. Raw data, intensity files and post-QC Plink files. Illumina HumanOmni2-5_8v1_A 78
EGAD00010001048 APCDR AGV Project: Array data from 79 Jola. Raw data, intensity files and post-QC Plink files. Illumina HumanOmni2-5_8v1_A 79
EGAD00010001047 APCDR AGV Project: Array data from 107 Ethiopians (Amhara, Oromo, Somali; subset of Ethiopian Genome Project Genotyping). Raw data, intensity files and post-QC Plink files. Illumina HumanOmni2-5_8v1_A 107
EGAD00010001221 Illumina Omni 2.5M SNPchip data (build37) of Ethiopian samples from the Pagani et al. 2015 AJHG paper (doi: http://dx.doi.org/10.1016/j. ajhg.2015.04.019) Illumina HumanOmni2-5_8v1_A 124
EGAD00010001223 Illumina Omni 2.5M SNPchip data (build37) of Egyptian samples from the Pagani et al. 2015 AJHG paper (doi: http://dx.doi.org/10.1016/j. ajhg.2015.04.019) Illumina HumanOmni2-5M-8v1-1_B 100
EGAD00010000496 Genome-wide SNP genotyping of African rainforest hunter-gatherers and neighbouring agriculturalists Illumina HumanOmni1-Quad-Illumina GenomeStudio 260
EGAD00010001287 Array methylation profiling of knee osteoarthritis patients who have undergone total joint replacement Illumina HumanMethylation450K 68
EGAD00010001291 Methylation profiling of hip osteoarthritis patients who have undergone total joint replacement Illumina HumanMethylation450K 27
EGAD00010000254 CLL Methylation Arrays Illumina HumanMethylation450 165
EGAD00010001040 Methylation changes in OA patients with chronic exposure to cobalt and chromium Illumina HumanMethylation450 68
EGAD00010001251 Epigenome of 36 rainforest hunther-gathering Baka of Cameroon by Illumina HumanMethylation450 array, used in the EGAS00001002226 study Illumina HumanMethylation450 38
EGAD00010001012 BLUEPRINT DNA Methylation 450K data of mantle cell lymphoma Illumina HumanMethylation 450K 86
EGAD00000000044 Northern Finland Birth Cohort 1966 samples Illumina HumanHap370 5,844
EGAD00000000043 GenomeEUtwin control samples Illumina HumanHap300-Duo, Illumina HumanHap 550K 2,099
EGAD00000000038 NcOEDG Stockholm 3 samples Illumina HumanHap 550 761
EGAD00000000030 T1DGC project 1958 British Birth Cohort samples Illumina HumanHap 550 2,604
EGAD00000000122 Genotypes at MITF E318K variant Illumina HumanHap 300 v2 Duo, Illumina HumanCNV370, Illumina Human660W-Quad 1,925
EGAD00000000042 GenomEUtwin Finnish (FIN) samples Illumina HumanHap 300 153
EGAD00000000032 NcOEDG Helsinki 1 samples Illumina HumanHap 300 19
EGAD00000000041 GenomEUtwin Swedish (SWE) samples Illumina HumanHap 300 302
EGAD00000000034 NcOEDG Helsinki 3 samples Illumina HumanHap 300 20
EGAD00000000033 NcOEDG Helsinki 2 samples Illumina HumanHap 300 180
EGAD00000000040 GenomEUtwin Danish (DK) samples Illumina HumanHap 300 162
EGAD00010000234 WTCCC2 samples from 1958 British Birth Cohort Illumina HumanExome-12v1_A-GenCall, zCall 12,241
EGAD00010000922 Subset 1 of osteoarthritis cases from the arcOGEN Consortium (http://www.arcogen.org.uk/) genotyped on HumanCoreExome-24v1-0 with broader consent. Illumina HumanCoreExome-24v1-0 494
EGAD00010000927 Subset 2 of osteoarthritis cases from the arcOGEN Consortium (http://www.arcogen.org.uk/) genotyped on HumanCoreExome-24v1-0 with consent for osteoarthritis studies only. Illumina HumanCoreExome-24v1-0 248
EGAD00010000926 Subset 1 of osteoarthritis cases from the arcOGEN Consortium (http://www.arcogen.org.uk/) genotyped on HumanCoreExome-12v1-1 with broader consent. Illumina HumanCoreExome-12v1-1 3,075
EGAD00010000924 Subset 2 of osteoarthritis cases from the arcOGEN Consortium (http://www.arcogen.org.uk/) genotyped on HumanCoreExome-12v1-1 with consent for osteoarthritis studies only. Illumina HumanCoreExome-12v1-1 991
EGAD00010001043 WTCCC3 Anorexia Nervosa Infinium-HumanCoreExome Illumina HumanCoreExome-12v1-0_A and HumanCoreExome-24v1-0_A 925
EGAD00010000918 Understanding Society GWAS, samples that passed quality control, imputed to UK10K + 1000 Genomes combined reference panel Illumina HumanCoreExome-12v1-0 chip, UK10K + 1000 Genomes combined reference panel imputed 9,944
EGAD00010000891 Understanding Society GWAS, samples that passed quality control Illumina HumanCoreExome-12v1-0 9,944
EGAD00010000923 Subset 2 of osteoarthritis cases from the arcOGEN Consortium (http://www.arcogen.org.uk/) genotyped on HumanCoreExome-12v1-0 with consent for osteoarthritis studies only. Illumina HumanCoreExome-12v1-0 463
EGAD00010000925 Subset 1 of osteoarthritis cases from the arcOGEN Consortium (http://www.arcogen.org.uk/) genotyped on HumanCoreExome-12v1-0 with broader consent. Illumina HumanCoreExome-12v1-0 855
EGAD00010000890 Understanding Society GWAS, all samples Illumina HumanCoreExome-12v1-0 10,463
EGAD00010001034 WTCCC3 Anorexia Nervosa GWAS Illumina Human670-QuadCustom_v1_A 1,696
EGAD00010000854 WTCCC3 UK maternal cases of pre-eclampsia Illumina Human670-QuadCustom_v1 1,990
EGAD00010000448 Macrophage Gene Expression Illumina Human-Ref-8 v3 beadchip 758
EGAD00010000446 Monocyte Gene Expression Illumina Human-Ref-8 v3 beadchip 758
EGAD00010000389 Cambridge control samples using a 24k expression array from Illumina Illumina Human-Ref 8 v3.0 expression array 395
EGAD00010000944 Genotyping data from Southeast Borneo individuals Illumina Human Omni Express Bead Chip-24 v1.0 41
EGAD00010000887 Freeze 1 of the RP3 project Illumina Human Methylation 450k BeadChip 3,898
EGAD00010001416 BBMRI - BIOS project - Freeze 2 - methylation Illumina Human Methylation 450k BeadChip 4,386
EGAD00010000789 ATRT expression Illumina Human HT6-v3 Array 4
EGAD00010000790 ATRT expression Illumina Human HT6-v3 Array 41
EGAD00010000450 Genome Wide Genotype Data Illumina Human Custom 1,2M and Human 610 Quad Custom arrays 758
EGAD00010001005 Illumina HumanCoreExome-12v1-1_A chip typing in a Greek adolescent population Illumina Human Core Exome 12v1.1 120
EGAD00010001157 Genotyping of additional Inflammatory Bowel Disease cases - 2014 (QC pass samples) Illumina Human Core Exome 12v1-1_a 9,247
EGAD00010001158 Genotyping of additional Inflammatory Bowel Disease cases - 2014 (all samples) Illumina Human Core Exome 12v1-1_a 11,767
EGAD00010000391 Cambridge control samples using a 660K genotyping chip from Illumina Illumina Human 660K Quad BeadChips - Illuminus 232
EGAD00010000387 Cambridge control samples using a 1.2M genotyping chip from Illumina Illumina Human 1.2M Duo custom BeadChips v1 - Genome Studio 188
EGAD00010000434 Normalised mRNA expression Illumina HT 12 1,302
EGAD00010000436 Illumina HT 12 IDAT files Illumina HT 12 1,302
EGAD00010000268 Metabric breast cancer samples (Expression raw data) Illumina HT 12 543
EGAD00010000212 Normalized expression data; normals Illumina HT 12 144
EGAD00010000211 Normalized expression data; validation set Illumina HT 12 995
EGAD00010000162 Illumina HT 12 IDATS Illumina HT 12 2,136
EGAD00010000210 Normalized expression data; discovery set Illumina HT 12 997
EGAD00010000160 Illumina HT 12 IDATS Illumina HT 12 1,001
EGAD00010001315 Single cell transcriptomics of PBMCs of 47 donors from the Lifelines Deep cohort (general population, Northern part of the Netherlands). Cells of five or six different donors were pooled together in one sample pool, resulting in eight different sample pools. In total, 28.855 cells were captured and their transcriptomes were sequenced to an average depth of 74k. Genotype data was available for each donor, which allowed us to use the Demuxlet method that uses variable SNPs between the pooled individuals to determine which cell belongs to which individual. Since genotype information is lacking of 2 individuals, the transcriptome of only 45 individuals could be retrieved. Illumina HiSeq4000 45
EGAD00010001403 Gene expression read counts Illumina HiSeq2000 132
EGAD00001002732 DNA methylation was analyzed for stem/progenitor cell types and terminally differentiated cell types of the human blood lineage (HSC, MPP, CMP, MEP, GMP, CLP, MLP0, MLP1, MLP2, MLP3, MK, CD4+ Tcell, CD8+ Tcell, Bcell, NK, Neut, Mono). Illumina HiSeq 4000;ILLUMINA 63 bam
EGAD00001002733 Gene expression was analyzed for stem/progenitor cell types and terminally differentiated cell types of the human blood lineage (HSC, MPP, CMP, GMP, CLP, MLP0, MLP1, MLP2, MLP3). Illumina HiSeq 4000;ILLUMINA 13 bam
EGAD00001002726 Cluster headache is a relatively rare headache disorder, typically characterized by multiple daily, short-lasting attacks of excruciating, unilateral (peri-)orbital or temporal pain associated with autonomic symptoms and restlessness. To better understand the pathophysiology of cluster headache, we used RNA sequencing to identify differentially expressed genes and pathways in whole blood of patients with episodic (n = 19) or chronic (n = 20) cluster headache in comparison with headache-free controls (n = 20). Illumina HiSeq 4000;ILLUMINA 60
EGAD00001003278 Whole Exome and Target Sequencing Data in 75 Samples from 5 Hepatocellular Carcinoma Patients. The sequencing was performed by Illumina HiSeq 4000. Background and aims: Intratumoral heterogeneity (ITH) challenges identifying mutations with target therapy potential whereas circulating cell-free DNAs (cfDNAs) could reflect nearly the entire mutation spectrum in given tumors. We investigated how to minimize the limit of ITH for profiling hepatocellular carcinoma (HCC).Methods: Thirty-two multi-regional HCC samples from five patients were subjected to whole exome sequencing (WES) and targeted deep sequencing (TDS). ITH extent was measured by the average percentage of non-ubiquitous mutations (present in parts of tumor regions). Matched cfDNAs were also analyzed by WES and TDS. Profiling efficiencies of single tumor specimen and cfDNA were compared and the one better depicted mutational landscape was selected to screen therapeutic targets.Results: We found variable extents of ITH in HCCs and observed branched and parallel evolution patterns. ITH level decreased at higher sequencing depth of TDS than that measured by WES (28.1% vs 34.9%, P < 0.01) but it remained unchanged upon additional samples analyzed. TDS of single tumor specimen detected an average of 70% the total mutations in HCC. Although more mutations were detected in cfDNA under TDS than WES, an average of 47.2% total HCC mutations uncovered by cfDNA suggested tissue outperform cfDNA and the latter may serve as alternative in profiling HCC genome. Consequently, TDS of single tumor tissue in 66 patients and cfDNAs in four unresectable HCCs identified 38.6% (26/66 and 1/4) patients bearing therapeutic targets.Conclusions: TDS of single tumor specimen could largely circumvent ITH to uncover mutations indicative of target therapy in HCC. Illumina HiSeq 4000;ILLUMINA 124
EGAD00001003399 RNAseq dataset of 34 samples (6 normals, 7 stroma-enriched, 21 malignant cells-enriched) from patients with resected pancreatic ductal carcinoma. Illumina HiSeq 4000;ILLUMINA 34
EGAD00001002269 We expressed PDGFRAmut, wild-type PDGFRA and a GFP control from lentivirus, in two primary GBM patient-derived cell lines that we had cultured as monolayers. Illumina HiSeq 4000; 1 fastq
EGAD00001002727 1,591 single cells from 11 colorectal cancer patients were profiled using Fluidigm based single cell RNA-seq protocol to characterized cellular heterogeneity of colorectal cancer. 630 single cells from 7 cell lines were profiled similarly to benchmark de novo cell type identification algorithms. Illumina HiSeq 3000;ILLUMINA 2,221
EGAD00001003302 Illumina HiSeq 3000;ILLUMINA 21
EGAD00001002110 Chronic lymphocytic leukemia (CLL) is characterized by substantial clinical heterogeneity, despite relatively few genetic alterations. To provide a basis for studying epigenome deregulation in CLL, we established genome-wide chromatin accessibility maps for 88 CLL samples from 55 patients using the ATAC-seq assay, and we also performed ChIPmentation and RNA-seq profiling for ten representative samples. Based on the resulting dataset, we devised and applied a bioinformatic method that links chromatin profiles to clinical annotations. Our analysis identified sample-specific variation on top of a shared core of CLL regulatory regions. IGHV mutation status – which distinguishes the two major subtypes of CLL – was accurately predicted by the chromatin profiles, and gene regulatory networks inferred for IGHV-mutated vs. IGHV-unmutated samples identified characteristic differences between these two disease subtypes. In summary, we discovered widespread heterogeneity in the chromatin landscape of CLL, established a community resource for studying epigenome deregulation in leukemia, and demonstrated the feasibility of chromatin accessibility mapping in cancer cohorts and clinical research. Illumina HiSeq 3000; 138 bam
EGAD00001002747 Whole-exome sequencing (WES) of 216 breast cancer metastasis-normal pairs from patients who underwent a biopsy in the context of the SAFIR01, SAFIR02, SHIVA or MOSCATO prospective trials (France). Illumina HiSeq 2500;ILLUMINA, NextSeq 500;ILLUMINA, Illumina HiSeq 4000;ILLUMINA 432
EGAD00001003121 Dataset is composed of FASTQ files from 165 samples of small round cell sarcomas which were RNA-sequenced (whole transcriptome) with either Illumina HiSeq 2500 (120 million reads per sample, paired-end 100 pb) or Illumina NextSeq 500 (110 million reads per sample, paired-end 150) Illumina HiSeq 2500;ILLUMINA, NextSeq 500;ILLUMINA 165
EGAD00001003414 June 2017 data update (bam/fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2500;ILLUMINA, NextSeq 500;ILLUMINA 40
EGAD00001003130 Whole exome sequencing data for patients with Bosma arhinia microphthalmia syndrome (BAMS). The dataset includes 21 samples from 7 families with BAMS; see Gordon et al, Nature Genetics, 2017. Illumina HiSeq 2500;ILLUMINA, Illumina HiSeq 4000;ILLUMINA 21
EGAD00001003594 This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ This dataset contains all the data available for this study on 2017-08-29. Illumina HiSeq 2500;ILLUMINA, Illumina HiSeq 4000;ILLUMINA 391
EGAD00001003800 Whole Exome Sequencing was performed in a dilution series containing known amounts of human and mouse DNA, 3x 100% human 0% mouse, 2x 90/10, 3x 50/50, 2x 25/75 and 3x 0/100. A set of breast cancer clinical samples, matched normal tissue and matched PDTXs (total number = 14) were also analysed. Paired-end 75bp sequences for the dilution series and paired-end 125bp for the clinical samples were obtained on Illumina HiSeq2500; fastq files are provided. A triplicate analysis of the transcriptome using RNA-seq was also performed for the Universal Human RNA Reference and the Universal Mouse RNA Reference samples. Paired-end 150bp fastq files obtained on Illumina HiSeq4000 are provided. Illumina HiSeq 2500;ILLUMINA, Illumina HiSeq 4000;ILLUMINA 12
EGAD00001001094 Raw Fastq files for 124 CPCGene Tumour/Normal Pairs from the 200PG Study Illumina HiSeq 2500;ILLUMINA, Illumina HiSeq 2500; 247 fastq
EGAD00001002256 Corresponding data set is composed of whole exome sequencing of Korean ER positive breast cancer under 35. This set provides 100 alignment files from normal-tumor paired whole exome sequencing of 50 patients. This is a part of total project data set. Illumina HiSeq 2500;ILLUMINA, Illumina HiSeq 2500; 100 bam
EGAD00001002685 Breast cancer PDTX sequencing data from Bruna et al, Cell 2016 - Exome Sequencing - Shallow Whole Genome Sequencing - RRBS Methylation Sequencing Illumina HiSeq 2500;ILLUMINA, Illumina HiSeq 2500; 393 bam
EGAD00001002705 McGill EMC Release 6 data Illumina HiSeq 2500;ILLUMINA 343 fastq
EGAD00001003550 Cell line exome sequencing Illumina HiSeq 2500;ILLUMINA 176
EGAD00001001885 January 2016 update of RNA-Seq data (bams, fastqs) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2500;ILLUMINA 17 fastq,bam
EGAD00001002767 A KNIH008 miRNA-seq single end data for adipocytes Illumina HiSeq 2500;ILLUMINA 1 fastq
EGAD00001002768 A KNIH009 miRNA-seq single end data for preadipocytes Illumina HiSeq 2500;ILLUMINA 1 fastq
EGAD00001002770 A KNIH011 miRNA-seq single end data for podocytes Illumina HiSeq 2500;ILLUMINA 1 fastq
EGAD00001001958 March 2016 update of whole genome shotgun sequencing data (bam/fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2500;ILLUMINA 17 fastq,bam
EGAD00001001959 March 2016 update of smRNA-Seq assays data (bam/fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2500;ILLUMINA 20 fastq,bam
EGAD00001002760 A KNIH001 miRNA-seq single end data for islet cells Illumina HiSeq 2500;ILLUMINA 1 fastq
EGAD00001002766 A KNIH007 miRNA-seq single end data for adipocytes Illumina HiSeq 2500;ILLUMINA 1 fastq
EGAD00001002764 A KNIH005 miRNA-seq single end data for islet cells Illumina HiSeq 2500;ILLUMINA 1 fastq
EGAD00001002239 June 2016 data update (bam/fastq for CEMT0062, CEMT0068, CEMT0072, CEMT0086, CEMT0087 ChIP-Seq and RNA-Seq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2500;ILLUMINA 10 bam,fastq
EGAD00001002275 We performed bulk exome-seq on a primary GBM and a blood sample from SF10282 Illumina HiSeq 2500;ILLUMINA 1 fastq
EGAD00001002274 We performed bulk exome-seq on a primary GBM and a blood sample from SF10360 Illumina HiSeq 2500;ILLUMINA 1 fastq
EGAD00001002273 We performed bulk exome-seq on a primary GBM and a blood sample from SF10345 Illumina HiSeq 2500;ILLUMINA 1 fastq
EGAD00001002271 We collected fresh tissue from an untreated GBM (SF10345) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells. Illumina HiSeq 2500;ILLUMINA 1 fastq
EGAD00001002272 We collected fresh tissue from an untreated GBM (SF10360) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells. Illumina HiSeq 2500;ILLUMINA 1 fastq
EGAD00001002658 Highly purified mesenchymal cells (CD45-/7AAD-/CD235a-/CD31-/CD271+/CD105+) were prospectively FACS-isolated from bone marrow specimens of 45 low-risk myelodysplastic syndrome (LRMDS) cases. Gene expression profiles (GEPs) of the 45 LRMDS have been compared to GEPs derived from likewise highly purified mesenchymal cells obtained from bone marrow specimens of healthy donors for the identification of inflammatory signatures. Additionally, an overlap in inflammatory signatures has been determined by comparing the GEPs of these 45 LRMDS cases to the GEPs of 4 Shwachman-Diamond syndrome and 3 Diamond-Blackfan anemia cases, both representing different subclasses of congenital pre-leukemia syndromes with a tendency of leukemic progression and perturbed niche compartment. Finally, the GEPs and gene expression signatures have been utilized for prognostication and the prediction of leukemic progression. Illumina HiSeq 2500;ILLUMINA 45 fastq
EGAD00001002660 Highly purified mesenchymal cells (CD45-/7AAD-/CD235a-/CD31-/CD271+/CD105+) were prospectively FACS-isolated from bone marrow specimens of 4 Shwachman-Diamond syndrome (SDS) cases. This data set, comprising 4 SDS cases, is used as complement to 45 low-risk myelodysplastic syndrome (LRMDS) and 3 Diamond-Blackfan anemia (DBA) cases to demonstrate aberrant inflammatory signaling as a common mechanism in pre-leukemia syndromes to induce genotoxic stress in hematopoietic stem cells. In addition this data set is used to determine different overlapping gene expression signatures in pre-leukemia syndromes compared to gene expression profiles of highly purified mesenchymal cells of healthy donors. Illumina HiSeq 2500;ILLUMINA 4 fastq
EGAD00001002659 Highly purified mesenchymal cells (CD45-/7AAD-/CD235a-/CD31-/CD271+/CD105+) were prospectively FACS-isolated from bone marrow specimens of 10 healthy donors (HDs). This data set is used as a baseline control to observe the differences between gene expression profiles (GEPs) of pre-leukemia cases (45 low-risk myelodysplastic syndrome, 4 Shwachman-Diamond and 3 Diamond-Blackfan anemia patients) and gene expression patterns observed in a normal, healthy context. Through differential expression and gene set enrichment analysis we determined that inflammatory signaling pathways are significantly more active in mesenchymal cells of pre-leukemia cases compared to their healthy counterparts. Finally, we determined through statistical modelling of healthy donor's GEPs which pre-leukemia cases have significantly more active inflammatory signaling and demonstrated a strong relation to survival statistics. Illumina HiSeq 2500;ILLUMINA 10 fastq
EGAD00001002722 Exome sequencing for 26 patients with matched blood RNA-seq for 41 patients Illumina HiSeq 2500;ILLUMINA 93 fastq
EGAD00001002724 September 2016 data update (bam/fastq/vcf) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2500;ILLUMINA 24 fastq,vcf,bam
EGAD00001002761 A KNIH002 miRNA-seq single end data for islet cells Illumina HiSeq 2500;ILLUMINA 1 fastq
EGAD00001002762 A KNIH003 miRNA-seq single end data for islet cells Illumina HiSeq 2500;ILLUMINA 1 fastq
EGAD00001002763 A KNIH004 miRNA-seq single end data for islet cells Illumina HiSeq 2500;ILLUMINA 1 fastq
EGAD00001002661 Highly purified mesenchymal cells (CD45-/7AAD-/CD235a-/CD31-/CD271+/CD105+) were prospectively FACS-isolated from bone marrow specimens of 3 Diamond-Blackfan anemia (DBA) cases. This data set, comprising 3 DBA cases, is used as complement to 45 low-risk myelodysplastic syndrome (LRMDS) and 4 Shwachman-Diamond syndrome (SDS) cases to demonstrate aberrant inflammatory signaling as a common mechanism in pre-leukemia syndromes to induce genotoxic stress in hematopoietic stem cells. In addition, this data set is used to determine different overlapping gene expression signatures in pre-leukemia syndromes compared to gene expression profiles of highly purified mesenchymal cells of healthy donors. Illumina HiSeq 2500;ILLUMINA 3 fastq
EGAD00001003122 December 2016 data update (bam/fastq for WGBS on samples CEMT0062, CEMT0068, CEMT0072, CEMT0086, CEMT0087) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2500;ILLUMINA 5
EGAD00001002769 A KNIH010 miRNA-seq single end data for podocytes Illumina HiSeq 2500;ILLUMINA 1 fastq
EGAD00001002765 A KNIH006 miRNA-seq single end data for beta cells Illumina HiSeq 2500;ILLUMINA 1 fastq
EGAD00001003098 Low-coverage sequencing data from 99 Lebanese samples Illumina HiSeq 2500;ILLUMINA 99 cram
EGAD00001001100 DCC Project Code: SKCA-BR Skin Adenocarcinoma - BR Brazil Illumina HiSeq 2500;ILLUMINA 200
EGAD00001003116 Benchmark data set containing five tumor/normal pairs of non-small cell lung cancer (NSCLC) patients. Tissue pairs were screened with bisulfite (BS) sequencing, MeDIP methylation enrichment sequencing and RNA sequencing in order to identify differentially methylated and expressed spots in the genomes. Illumina HiSeq 2500;ILLUMINA 10
EGAD00001003111 We collected fresh tissue from an untreated GBM directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine after selection of CD11b+ cells using magnetic beads. Illumina HiSeq 2500;ILLUMINA 1
EGAD00001003110 We collected fresh tissue from an untreated GBM directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine after selection of CD11b+ cells using magnetic beads. Illumina HiSeq 2500;ILLUMINA 1
EGAD00001003114 We collected fresh tissue from an untreated GBM (SF10281) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells. Illumina HiSeq 2500;ILLUMINA 1
EGAD00001003112 We collected fresh tissue from an untreated GBM (SF10592) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells. Illumina HiSeq 2500;ILLUMINA 1
EGAD00001003107 We collected fresh tissue from an untreated GBM directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine after selection of CD11b+ cells using magnetic beads. Illumina HiSeq 2500;ILLUMINA 1
EGAD00001003108 We collected fresh tissue from an untreated GBM directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine after selection of CD11b+ cells using magnetic beads. Illumina HiSeq 2500;ILLUMINA 1
EGAD00001003109 We collected fresh tissue from an untreated GBM directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine after selection of CD11b+ cells using magnetic beads. Illumina HiSeq 2500;ILLUMINA 1
EGAD00001003113 We collected fresh tissue from an untreated GBM (SF10679) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells. Illumina HiSeq 2500;ILLUMINA 1
EGAD00001003204 Understanding how cells sense and respond to their environment, and how these responses are modulated by genetic variation, are fundamental biological problems, particularly for understanding how pathogenic organisms invade and manipulate the cells of the human immune system. Macrophages recognize and respond to many important human pathogens including HIV-1, Mycobacteria tuberculosis and Salmonella. This study will focus on the cellular response of human macrophages to Salmonella infection and how this response is modulated by the genetic bacground of the individual as well as additional pro-inflammatory stimulus (interferon-gamma priming). We will acquire 100 human induced pluripotent stem cell lines from the HipSci project, differentiate the cells in vitro into macrophages and expose them to four environmental conditions: (i) no stimulation, (ii) interferon-gamma (18h), (iii) Salmonella typhimurium SL1344 (5h), (iv) interferon-gamma (18h) + Salmonella (5h).Subsequently, we will isolate RNA from the samples for sequencing. Illumina HiSeq 2500;ILLUMINA 236
EGAD00001003151 Bulk whole-genome BAM files for 184-hTERT-L2, SA501X3F, and SA501X4F. Illumina HiSeq 2500;ILLUMINA 3
EGAD00001003150 Microfluidic direct library preparation (DLP) single-cell whole-genome BAM files for fourth-passage patient-derived primary triple-negative breast cancer xenograft SA501X4F. Illumina HiSeq 2500;ILLUMINA 384
EGAD00001003152 Microfluidic direct library preparation (DLP) single-cell whole-genome BAM files for near-diploid immortalized breast epithelial cell line 184-hTERT-L2. Illumina HiSeq 2500;ILLUMINA 192
EGAD00001003149 Microfluidic direct library preparation (DLP) single-cell whole-genome BAM files for third-passage patient-derived primary triple-negative breast cancer xenograft SA501X3F. Illumina HiSeq 2500;ILLUMINA 384
EGAD00001003213 The olfactory gene repertoire is largely species-specific, shaped by the nature and necessity of chemosensory information for survival in each species' niche. We are intrigued by this interspecific variation and started to investigate the olfactory transcriptome in primates for evidence of selection at the level of receptor gene choice. Having collected this data from two primates, we now wish to extend the analysis to humans. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina HiSeq 2500;ILLUMINA 9
EGAD00001003217 Targeted resequencing at high depth (21 genes, 9 chromosomal regions): at least 4 FFPE samples per case and matched germline DNA: * 100 cases with detailed outcome data, including 15 cases with tumour relapse (515 samples) * 40 cases with matched pre-chemotherapy biopsies (240 samples) * 50 nephrogenic rests matched to above cases (50 samples) We expect a proportion (possibly 10%) of cases to be mutationally silent on the above studies, and propose to subsequently carry out integrated whole-genome, methylome and transcriptome studies on matched frozen tissue from these cases Illumina HiSeq 2500;ILLUMINA 35
EGAD00001003200 Files from whole exome sequencing of 26 tumors and two matched normals from one melanoma patient. The 26 tumors include the untreated primary, cutaneous metastases and distant metastases to internal organs. Illumina HiSeq 2500;ILLUMINA 28
EGAD00001003245 We aim to sequence the small RNAs of 22 human melanoma cell lines in biological triplicate in order to define the microRNAs expression profile of each cell line. The data will be correlated to the mutation status and the sensitivity to a panel of drugs in order to identify genes whose deregulation is associated to drug resistance This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina HiSeq 2500;ILLUMINA 66
EGAD00001003255 Transcriptome of anaplastic meingiomas Illumina HiSeq 2500;ILLUMINA 34
EGAD00001003254 R&D project to develop low input library construction methods. Illumina HiSeq 2500;ILLUMINA 12
EGAD00001003246 Whole exome sequencing of hepatosplenic T cell lymphoma (HSTL) tumors, paired normals, and cell lines, including (1) 68 exome capture, paired-end Illumina Hiseq sequencing, BAM files from HSTL tumor samples, (2) 20 exome capture, paired-end Illumina Hiseq sequencing, BAM files from HSTL paired normal samples, and (3) 2 exome capture, paired-end Illumina Hiseq sequencing, BAM files from HSTL cell lines. Illumina HiSeq 2500;ILLUMINA 90
EGAD00001003272 March 2017 data update (bam/fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2500;ILLUMINA 8
EGAD00001003284 Whole exome sequencing of enteropathy-associated T cell lymphoma (EATL) tumors and paired normals, as well as RNA-sequencing of EATL tumors: including (1) 69 exome capture, paired-end Illumina Hiseq sequencing, BAM files from EATL tumor samples, (2) 36 exome capture, paired-end Illumina Hiseq sequencing, BAM files from EATL paired normal samples, and (3) 32 RNAseq, paired-end Illumina Hiseq sequencing, BAM files from EATL tumor samples. Illumina HiSeq 2500;ILLUMINA 137
EGAD00001003193 Exome sequencing for 2 infertile brothers Illumina HiSeq 2500;ILLUMINA 2
EGAD00001003293 RNA-Seq and WXS from 6 glioblastoma patients Illumina HiSeq 2500;ILLUMINA 11
EGAD00001003335 A resource for assessment of exon CNV calling methods in targeted NGS data, we here present the ICR96 exon CNV validation series. The dataset includes high-quality sequencing data from a targeted NGS assay (the TruSight Cancer Panel) together with Multiplex Ligation-dependent Probe Amplification (MLPA) results for 96 independent samples. 66 samples contain at least one validated exon CNV and 30 samples have validated negative results for exon CNVs in 26 genes. The dataset includes 46 exon CNVs in BRCA1, BRCA2, TP53, MLH1, MSH2, MSH6, PMS2, EPCAM and PTEN, giving excellent representation of the cancer predisposition genes most frequently tested in clinical practice. Moreover, the validated exon CNVs include 25 single exon CNVs the most difficult exon CNV to detect. Illumina HiSeq 2500;ILLUMINA 96
EGAD00001003138 A dataset consisting of Multi-regional Whole Exome Sequencing (WES) and Whole Genome Sequencing (WGS) data for 54 samples from 9 patients with hepatocellular carcinoma. The dataset includes 45 tumor samples and 9 normal blood samples. Selected somatic variants were validated by Sequenom. Patients covered are: Patient 1, Patient 2, Patient 3, Patient 4, Patient 5, Patient 6, Patient 7, Patient 8, Patient 9 and Patient 10. Illumina HiSeq 2500;ILLUMINA 54
EGAD00001003161 HipSci - Bardet-Biedl Syndrome - Exome Sequencing - October 2016 Illumina HiSeq 2500;ILLUMINA 38
EGAD00001003798 October 2017 data update (bam/fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2500;ILLUMINA 28
EGAD00001003354 From 9 patients undergoing hip joint replacement surgery for osteoarthritis, we collected 3 cartilage samples each: a low-grade sample (no obvious evidence of damage or fibrillation); a high-grade sample (damaged and fibrillated cartilage); an osteophytic sample (overlaid bony protrusions mainly around the margins of the articular surface). Multiplexed libraries were sequenced on Illumina HiSeq 2000 (75bp paired-end read length) and a cram file was produced for each sample. This dataset contains all the data available for this study on 2017-06-09. Illumina HiSeq 2500;ILLUMINA 27
EGAD00001003355 From 17 patients undergoing knee joint replacement surgery for osteoarthritis, we collected 4 samples each: intact cartilage, degraded cartilage, synovium, and meniscus. We also collected blood for DNA analysis. Multiplexed libraries were sequenced on Illumina HiSeq 2000 (75bp paired-end read length) and a cram file was produced for each sample. This dataset contains all the data available for this study on 2017-06-09. Illumina HiSeq 2500;ILLUMINA 72
EGAD00001003351 In order to comprehensively investigate the genetic relationship between PTC tumors and benign nodules, we totally collected 127 fresh-frozen biopsies samples from 28 patients with concurrent thyroid benign nodule and PTC (n=20) or simple benign nodule (n=8). We carried out whole-exome sequencing on all the 127 biopsies samples and RNA-sequencing in total of 40 samples. Illumina HiSeq 2500;ILLUMINA 127
EGAD00001003422 WXS from barcoded cells that are FACS sorted from GBM-719 xenografts, and the germline reference from patient GBM-719. The 4 xenografts are named according to passage (secondary or tertiary) and treatment (vehicle control or temozolomide). Illumina HiSeq 2500;ILLUMINA 5
EGAD00001003443 Massively parallel nanowell-based single-cell gene expression profiling Illumina HiSeq 2500;ILLUMINA 14
EGAD00001003797 This dataset contains WES data (.bam files) and associated phenotype information from 10 patients included in our microbiome study who went on to anti PD-1 immunotherapy for the treatment of metastatic melanoma at the University of Texas MD Anderson Cancer Center. Both tumor and matching germ line normal were sequenced on each patient using Illumina HiSeq 2500. The average coverage was 283X in tumors and 135X in germline (tumor+germline overall:209, Range: 0-1552). Illumina HiSeq 2500;ILLUMINA 20
EGAD00001003483 A CKD25_C_Podo_mRNA-Seq paired end data for Podocytes(CD90(-) Podocalyxin(+), kidney) Illumina HiSeq 2500;ILLUMINA 1
EGAD00001003487 A OB57_D_PreA_mRNA-Seq paired end data for Preadipocyte(fat) Illumina HiSeq 2500;ILLUMINA 1
EGAD00001003482 A CKD24_C_Podo_mRNA-Seq paired end data for Podocytes(CD90(-) Podocalyxin(+), kidney) Illumina HiSeq 2500;ILLUMINA 1
EGAD00001003488 A IPS01_N_Fibroblast_mRNA-Seq paired end data for iPSC(Oct4) Illumina HiSeq 2500;ILLUMINA 1
EGAD00001003501 A IPS01_N_Fibroblast_smRNA-Seq single end data for iPSC(Oct4) Illumina HiSeq 2500;ILLUMINA 1
EGAD00001003491 A IPS04_X_Fibroblast_mRNA-Seq paired end data for iPSC(Oct4) Illumina HiSeq 2500;ILLUMINA 1
EGAD00001003497 A CKD23_C_Mesan_smRNA-Seq single end data for Mesangial cells(kidney) Illumina HiSeq 2500;ILLUMINA 1
EGAD00001003481 A CKD23_C_Mesan_mRNA-Seq paired end data for Mesangial cells(kidney) Illumina HiSeq 2500;ILLUMINA 1
EGAD00001003495 A OB56_N_PreA_smRNA-Seq single end data for Preadipocytes(fat) Illumina HiSeq 2500;ILLUMINA 1
EGAD00001003494 A DB31_N_Alpha_smRNA-Seq single end data for alpha cells(PSA-NCAM(-), pancreas) Illumina HiSeq 2500;ILLUMINA 1
EGAD00001003496 A OB57_D_PreA_smRNA-Seq single end data for Preadipocyte(fat) Illumina HiSeq 2500;ILLUMINA 1
EGAD00001003485 A DB31_N_Alpha_mRNA-Seq paired end data for alpha cells(PSA-NCAM(-), pancreas) Illumina HiSeq 2500;ILLUMINA 1
EGAD00001003484 A CKD27_C_Mesan_mRNA-Seq paired end data for Mesangial cells(kidney) Illumina HiSeq 2500;ILLUMINA 1
EGAD00001003504 A IPS04_X_Fibroblast_smRNA-Seq single end data for iPSC(Oct4) Illumina HiSeq 2500;ILLUMINA 1
EGAD00001003489 A IPS02_N_NPC_mRNA-Seq paired end data for Neural progenitor cells(Nestin) Illumina HiSeq 2500;ILLUMINA 1
EGAD00001003490 A IPS03_N_ENeuron_mRNA-Seq paired end data for Early neuron cells(Tuj1) Illumina HiSeq 2500;ILLUMINA 1
EGAD00001003506 A IPS06_X_ENeuron_smRNA-Seq single end data for Early neuron cells(Tuj1) Illumina HiSeq 2500;ILLUMINA 1
EGAD00001003499 A CKD25_C_Podo_smRNA-Seq single end data for Podocytes(CD90(-) Podocalyxin(+), kidney) Illumina HiSeq 2500;ILLUMINA 1
EGAD00001003492 A IPS05_X_NPC_mRNA-Seq paired end data for Neural progenitor cells(Nestin) Illumina HiSeq 2500;ILLUMINA 1
EGAD00001003486 A OB56_N_PreA_mRNA-Seq paired end data for Preadipocytes(fat) Illumina HiSeq 2500;ILLUMINA 1
EGAD00001003493 A IPS06_X_ENeuron_mRNA-Seq paired end data for Early neuron cells(Tuj1) Illumina HiSeq 2500;ILLUMINA 1
EGAD00001003502 A IPS02_N_NPC_smRNA-Seq single end data for Neural progenitor cells(Nestin) Illumina HiSeq 2500;ILLUMINA 1
EGAD00001003500 A CKD27_C_Mesan_smRNA-Seq single end data for Mesangial cells(kidney) Illumina HiSeq 2500;ILLUMINA 1
EGAD00001003505 A IPS05_X_NPC_smRNA-Seq single end data for Neural progenitor cells(Nestin) Illumina HiSeq 2500;ILLUMINA 1
EGAD00001003498 A CKD24_C_Podo_smRNA-Seq single end data for Podocytes(CD90(-) Podocalyxin(+), kidney) Illumina HiSeq 2500;ILLUMINA 1
EGAD00001003590 Ultra-Fast Patient-Derived Xenografts Identify Functional and Spatial Tumour Heterogeneities that Drive Therapeutic Resistance - WXS unaligned reads Illumina HiSeq 2500;ILLUMINA 27
EGAD00001003448 strand-specific RNA-seq data from 19 gastric tumors and their adjacent normal tissues, plus 16 gastric cancer cell lines, one normal gastric cell line, and 3 normal stomach RNAs Illumina HiSeq 2500;ILLUMINA 58
EGAD00001003409 Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are part of a clinical, pathological and genetic continuum. The purpose of the present study was to assess the mutation burden that is present in ALS and/or FTD known disease-causing genes in 54 patients (16 with available postmortem neuropathological diagnosis) with concurrent ALS and FTD (ALS/FTD) not-carrying the C9orf72 hexanucleotide repeat expansion, the most important genetic cause in both diseases. Illumina HiSeq 2500;ILLUMINA 54
EGAD00001003556 We will perform RNAseq to evaluate the effects of the loss of a list of TSGs on the transcriptome. This dataset contains all the data available for this study on 2017-08-10. Illumina HiSeq 2500;ILLUMINA 25
EGAD00001003564 The aim of the project is the definition of the molecular defect in a cohort of Rett-like patients negative for mutations in known disease genes. To this aim, a number of unrelated trios (patients plus parents) will be analysed by exome sequencing. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ This dataset contains all the data available for this study on 2017-08-16. Illumina HiSeq 2500;ILLUMINA 46
EGAD00001003565 The project is focused on the axonal forms of Charcot-Marie-Tooth (CMT) disease. We have selected 13 families (7 from Spain and 6 from Czech Republic) that have been indepth clinically assessed and previously tested for mutations in known CMT genes without causal variants characterised. In these patients we expect to discover several CMT2 genes. Thus, we requested for exome sequencing of 45 DNAs:27 exomes in families from Spain and 18 exomes in the families from Czech Republic. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ This dataset contains all the data available for this study on 2017-08-16. Illumina HiSeq 2500;ILLUMINA 45
EGAD00001003466 This dataset contains 21 tumor-normal pairs of exome sequencing data of HCC patient from Chang Gung Memorial Hospital, Taiwan. Illumina HiSeq 2500;ILLUMINA 42
EGAD00001003467 This dataset contains 77 tumor-normal pairs of exome sequencing data of HCC patient from National Taiwan University, Taiwan. Illumina HiSeq 2500;ILLUMINA 154
EGAD00001003430 RNA analysis of six patients 34, 35, 36, 37, 38 and 39 with WGS done on Illumina HiSeq2500. For research purpose and authorised user only. Illumina HiSeq 2500;ILLUMINA 6
EGAD00001003750 This is the first whole exome sequencing analysis of a primary meningeal melanocytic tumour (MMT) alongside the patients germline. Here we report the CRAM files from the tumour and germline. Illumina HiSeq 2500;ILLUMINA 2
EGAD00001003582 Genomics-Driven Precision Medicine for Advanced Pancreatic Cancer - Early Results from the COMPASS Trial - RNA-Seq unmapped reads Illumina HiSeq 2500;ILLUMINA 50
EGAD00001003746 Sequencing was performed using OncoPanel v.2 (OPv2), an Agilent SureSelect custom designed bait set consisting of the coding regions of 504 genes, previously linked to human cancer. Sequencing wa sperformed on an Illumina HiSeq 2500. 14 highly differentiated, fusion-negative rhabdomyosarcoma tumor samples, and 8 non-matched normal skeletal muscle samples weer sequenced. BAM files are available for download. Illumina HiSeq 2500;ILLUMINA 22
EGAD00001003503 A IPS03_N_ENeuron_smRNA-Seq single end data for Early neuron cells(Tuj1) Illumina HiSeq 2500;ILLUMINA 1
EGAD00001003602 Dataset consisting of: (1) N=234 genome-wide chromatin accessibility (ATAC-seq) profiles for distinct N=21 healthy old and N=28 healthy young subjects. ATAC-seq biological samples provided for the following tissues: PBMC (N=24), CD14+ monocytes (N=18), CD8+ memory T cells (N=7), CD8+ naive T cells (N=7), CD4+ memory T cells (N=7), CD4+ naive T cells (N=7), and naive B cells (N=7). (2) N=39 genome-wide transcription (RNA-seq) data for distinct N=15 healthy old and N=24 healthy young subjects' PBMCs. Illumina HiSeq 2500;ILLUMINA 273
EGAD00001003769 This dataset is a time-series of EGFR-mutant NSCLC clinical specimens from an individual patient profiled using tumor-based whole exome sequencing and the data is in BAM format. DNA was extracted from FFPE for primary tumor and frozen tumor tissue samples and matched non-tumor tissue using the Qiagen Allprep DNA/RNA Mini Kit.  The library preparation protocol was based on the Agilent SureSelect Library Prep and Capture System. DNA was resuspended in a low TE buffer and sheared (Duty Cycle 5%; Intensity 175; Cycles/Burst: 200; Time: 300s, Corvaris S2 Utrasonicator).  Bar-coded exome libraries were prepared using the Agilent Sure Select V5 library kit per manfucaturer’s specifications. The libraries were run on the HiSeq2500. Raw paired end reads (100bp) in FastQ format generated by the Illumina pipeline were aligned to the full hg19 genomic assembly obtained from USCS, gencode 14, using bwa version 0.7.12. Picard tools version 1.117 was used to sort, remove duplicate reads and generate QC statistics. Tumor DNA was sequenced to median depth of 303X (range 114.39-383.41) and the matched germline DNA to average depth of 231.65. Illumina HiSeq 2500;ILLUMINA 8
EGAD00001003600 Exome sequencing data for 1001 DLBCL patients and RNA sequencing data for 775 DLBCL patients Illumina HiSeq 2500;ILLUMINA 1,776
EGAD00001003759 ATAC-seq data for 5 non-diabetic human pancreatic islet samples Illumina HiSeq 2500;ILLUMINA 5
EGAD00001003780 RNA-seq data obtained from directed differentiation of a subset of FiPSCs and BiPSCs cell lines towards islet-like cells. RNA was collected at two key developmental stages: definitive endoderm (DE) and pancreatic progenitors (PP). Illumina HiSeq 2500;ILLUMINA 16
EGAD00001003792 The dataset for High Grade Serous Ovarian Carcinomas Originate in the Fallopian Tube includes 46 bam files from next-generation sequencing on the Illumina HiSeq2500. The samples analyzed include multiple lesions from nine patients, five with high grade serous ovarian carcinoma and four who are BRCA-carriers. Illumina HiSeq 2500;ILLUMINA 46
EGAD00001003793 By differential gene expression analysis followed by protein expression and functional studies, we define that the naive T cells having divided the least since thymic emigration express complement receptors (CR1 and CR2) known to bind complement C3b- and C3d-decorated microbial products and, following activation, produce IL-8 (CXCL8), a major chemoattractant for neutrophils in bacterial defense. We also observed an IL-8–producing memory T cell subpopulation coexpressing CR1 and CR2 and with a gene expression signature resembling that of RTEs. JCI Insight. 2017;2(16):e93739. https://doi.org/10.1172/jci.insight.93739 Illumina HiSeq 2500;ILLUMINA 24
EGAD00001001863 Exome data of PDX models. Illumina HiSeq 2500; 4 fastq
EGAD00001001301 Whole exome sequencing data of 5 patients diagnosed with FL that had undergone several relapse episodes without evidence of transformation Illumina HiSeq 2500; 29 bam
EGAD00001001285 McGill EMC Release 4 in tissue "Brodmann (1909) area 44" Illumina HiSeq 2500; 1 fastq
EGAD00001001296 McGill EMC Release 4 for assay "H3K4me1" Illumina HiSeq 2500; 41 fastq
EGAD00001001294 McGill EMC Release 4 for assay "H3K27me3" Illumina HiSeq 2500; 32 fastq
EGAD00001001287 McGill EMC Release 4 in tissue "kidney" Illumina HiSeq 2500; 2 fastq
EGAD00001001282 McGill EMC Release 4 in tissue "venous blood" for cell type "Monocyte" Illumina HiSeq 2500; 82 fastq
EGAD00001001292 McGill EMC Release 4 for assay "smRNA-seq": Transcriptome profiling by high-throughput sequencing Illumina HiSeq 2500; 6 fastq
EGAD00001001293 McGill EMC Release 4 for assay "ChIP-Seq Input" Illumina HiSeq 2500; 52 fastq
EGAD00001001290 McGill EMC Release 4 for assay "RNA-seq": Transcriptome profiling by high-throughput sequencing Illumina HiSeq 2500; 261 fastq
EGAD00001001280 McGill EMC Release 4 in tissue "venous blood" for cell type "CD4-positive, alpha-beta T cell" Illumina HiSeq 2500; 40 fastq
EGAD00001001298 McGill EMC Release 4 for assay "H3K27ac" Illumina HiSeq 2500; 36 fastq
EGAD00001001297 McGill EMC Release 4 for assay "H3K4me3" Illumina HiSeq 2500; 42 fastq
EGAD00001001278 McGill EMC Release 4 in tissue "venous blood" for cell type "B cell" Illumina HiSeq 2500; 41 fastq
EGAD00001001283 McGill EMC Release 4 in tissue "venous blood" for cell type "T cell" Illumina HiSeq 2500; 20 fastq
EGAD00001001277 McGill EMC Release 4 in tissue "fat pad" for cell type "fat cell" Illumina HiSeq 2500; 1 fastq
EGAD00001001295 McGill EMC Release 4 for assay "H3K36me3" Illumina HiSeq 2500; 37 fastq
EGAD00001001288 McGill EMC Release 4 in tissue "skeletal muscle tissue" Illumina HiSeq 2500; 29 fastq
EGAD00001000727 Targeted resequencing on the specific regions chr3:126036241-130672290 and chr3:157712147-175694147 in hg19 centered on the chromosomal regions 3q21 and 3q26 respectively. The focus lies on the detection of the exact breakpoints in Acute Myeloid Leukemia (AML) patients having acquired a inv(3)(q21q26) or t(3;3)(q21;q26). This dataset contains all information to detect all structural variants contained within these regions, including the 3q-aberrations inducing the overexpression of the proto-oncogene EVI1. Illumina HiSeq 2500; 38 fastq
EGAD00001000726 In total 30 Acute Myeloid Leukemias with an acquired inv(3)(q21q26) or t(3;3)(q21;q26) have been characterized by whole transcriptome sequencing (RNA-Seq). The 3q-aberration leads to overexpression of the proto-oncogene EVI1, but the mechanism of overexpression has thus far been elusive. The RNA-Seq was integral in determining the precise enhancer inducing the overexpression and led to other key discoveries. Illumina HiSeq 2500; 30 fastq
EGAD00001000872 These samples are to be analysed with the CGP Developed cancer panel and the results will be compared with WGS data from 4 different comercial providers. Illumina HiSeq 2500; 8 cram
EGAD00001000870 Testing logistics and infrastructure of molecular screening program. Core biopsies taken from invasive recurrent or metastatic breast cancer to evaluate and identify molecular traits rendering them suitable for clinical trials Illumina HiSeq 2500; 52 cram
EGAD00001000879 Genomic libraries will be generated from total genomic DNA derived from 200+ patients with childhood Transient Myeloproliferative Disorder (TMD) and or Acute Megakaryocytic Leukemia (AMKL) as well some matched constitutional samples (n < 50). Libraries will be enriched for a selected panel of genes using a bespoke pulldown protocol. 96 Samples will be individually barcoded and subjected to up to two lanes of Illumina HiSeq. Paired reads will be mapped to build 37 of the human reference genome to facilitate the characterisation of known gene mutations in cancer as well as the validation of potentially novel variants identified by prior exome sequencing. Illumina HiSeq 2500; 335 cram
EGAD00001000902 The dataset includes the targeted gene sequencing data from 51 pairs of gallbladder caner tissues and patient-matched normal tissues. Illumina HiSeq 2500; 102 bam
EGAD00001000901 The dataset includes the whole exome sequencing data from 32 pairs of gallbladder caner tissues and patient-matched normal tissues. Illumina HiSeq 2500; 64 bam
EGAD00001000972 Whole Genome Sequencing to track subclonal heterogeneity in 18 samples from 3 Chronic Lymphocytic Leukemia patients subjected to repeated cycles of therapy. Illumina HiSeq 2500; 18 bam
EGAD00001001115 SeqControl Illumina HiSeq 2500; 54 fastq
EGAD00001000997 Whole-exome sequencing of a chronic lymphocytic leukemia (CLL) developed during vemurafenib treatment of a patient with malignant melanoma. Peripheral blood mononuclear cells were separated by Ficoll gradient centrifugation. DNA was extracted from highly purified (>97%) CD19+CD5+ cells obtained from the patient while being under BRAF inhibition versus CD14+ germline control cells (>90% purity). No alterations that could be linked to aberrant RAS activity or paradoxical RAF/MEK/ERK signaling could be identified in the CLL, which shows characteristic copy number alterations. Illumina HiSeq 2500; 2 fastq
EGAD00001001021 Exome sequencing of 1000 samples from the UK 1958 Birth Cohort. DNA library preps prepared with Illumina TruSeq sample preparation kit. The captured DNA libraries were PCR amplified using the supplied paired-end PCR primers. Sequencing was performed with an Illumina HiSeq2000 (SBS Kit v3, one pool per lane) generating 2x101-bp reads. Illumina HiSeq 2500; 1,000 fastq
EGAD00001001031 These are only the whole exome sequences Illumina HiSeq 2500; 6 bam
EGAD00001001040 This is the complete dataset (exome and genome) for the EGAS00001000974 study. Illumina HiSeq 2500; 16 bam
EGAD00001001023 nccRCC Whole Exome sequencing data (consented samples only) Illumina HiSeq 2500; 137 fastq
EGAD00001001022 nccRCC RNA-Seq data of consented samples Illumina HiSeq 2500; 139 fastq
EGAD00001001047 Targeted exome sequencing of 375 genes Illumina HiSeq 2500; 31 fastq
EGAD00001000988 Validation/deeper sequencing for metastatic prostate cancer samples Illumina HiSeq 2500; 94 cram
EGAD00001000989 Validation/deeper sequencing for metastatic prostate cancer samples Illumina HiSeq 2500; 26 cram
EGAD00001000979 We are developing a protocol to differentiate mouse and human induced pluripotent stem (IPS) and embryonic stem (ES) cells towards the haematopoietic pathway to generate erythrocytes in vitro. This system has many applications such as the study of the role of specific genes and human polymorphisms in infectious diseases such as malaria, as well as haematological diseases such as myelodysplastic syndrome. The nature of the in vitro differentiation process means that a heterogeneous population of cells is generated. In order to understand the types of cells produced with our protocol, we have performed a single cell analysis, which has the power to reveal the different populations of cells and their characteristics. For this, a cDNA library has been made that needs to be sequenced to obtain the gene expression profiles of the different cells. With this information we will be able to assess the quality of the differentiation protocol and improve it in order to produce better cells for the downstream applications. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina HiSeq 2500; 192 cram
EGAD00001001928 This study will analyse the guide sequence which were used for making mutations in the Cas9-expressing cells. We used GeCKO v2 library which were released by Feng Zhang, 2014. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina HiSeq 2500; 61 cram
EGAD00001000894 SPECTA comprises a network of participating European clinical sites and NGS screening platforms that can screen individual patients for multiple molecular targets and potentially allow the design of trials that will match the specific biology of the diseases affecting specific patients with cancer. Illumina HiSeq 2500; 64 cram
EGAD00001001859 Raw fastq files for sequence data generated at 5 sequencing centers from a Medulloblastoma sample and matching blood normal control. Illumina HiSeq 2500; 2 fastq
EGAD00001001858 Raw fastq files from WGS sequencing of CLL and matching blood normal for the ICGC Techval Benchmark1 study. Sequence data was provided to multiple centers for independent analysis and comparison. Illumina HiSeq 2500; 2 fastq
EGAD00001001222 TGCT Whole Exome Sequencing data Illumina HiSeq 2500; 84 bam
EGAD00001001221 Illumina HiSeq 2500; 54 fastq
EGAD00001001363 To generate an RNA-Seq dataset for organoids apically stimulated with Salmonella Typhimurium. These data are part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina HiSeq 2500; 12 cram
EGAD00001001279 McGill EMC Release 4 in tissue "venous blood" for cell type "CD4-positive helper T cell" Illumina HiSeq 2500; 55 fastq
EGAD00001001284 McGill EMC Release 4 in tissue "Brodmann (1909) area 11" Illumina HiSeq 2500; 1 fastq
EGAD00001001276 McGill EMC Release 4 for cell type "induced pluripotent stem cell" Illumina HiSeq 2500; 8 fastq
EGAD00001001300 McGill EMC Release 4 for assay "ATAC-seq": Sequencing of transposase-accessible chromatin as described by Buenrostro et al. (Nature Methods 10, 1213?1218 (2013) doi:10.1038/nmeth.2688) Illumina HiSeq 2500; 1 fastq
EGAD00001001291 McGill EMC Release 4 for assay "mRNA-seq": Transcriptome profiling by high-throughput sequencing Illumina HiSeq 2500; 40 fastq
EGAD00001001289 McGill EMC Release 4 for assay "Bisulfite-seq": Methylation profiling by high-throughput sequencing Illumina HiSeq 2500; 44 fastq
EGAD00001001299 McGill EMC Release 4 for assay "H3K9me3" Illumina HiSeq 2500; 29 fastq
EGAD00001001286 McGill EMC Release 4 in tissue "Brodmann (1909) area 8;Brodmann (1909) area 9" Illumina HiSeq 2500; 1 fastq
EGAD00001001281 McGill EMC Release 4 in tissue "venous blood" for cell type "eosinophil" Illumina HiSeq 2500; 3 fastq
EGAD00001001302 Illumina HiSeq 2500; 2 bam
EGAD00001001356 Neuroblastoma, a clinically heterogeneous pediatric cancer, is characterized by distinct genomic profiles but few recurrent mutations. As neuroblastoma is expected to have high degree of genetic heterogeneity, study of neuroblastoma's clonal evolution with deep coverage whole-genome sequencing of diagnosis and relapse samples will lead to a better understanding of the molecular events associated with relapse. Samples were included in this study if sufficient DNA from constitutional, diagnosis and relapse tumors was available for WGS. Whole genome sequencing was performed on trios (constitutional, diagnose and relapse DNA) from eight patients using Illumina Hi-seq2500 leading to paired-ends (PE) 90x90 for 6 of them and 100x100 for two. Expected coverage for sample NB0175 100x100bp was 30X for tumor and constitutional samples. For the seven other patients expected coverage was 80X for tumor samples with PE 100x100, 100X in the other tumor samples and 50X for all constitutional samples (see table 1). Following alignment with BWA (Li et al., Oxford J, 2009 Jul) allowing up to 4% of mismatches, bam files were cleaned up according to the Genome Analysis Toolkit (GATK) recommendations (Van der Auwera et al., Current Protocols in Bioinformatics, 2013, picard-1.45, GenomeAnalysisTK-2.2-16). Variant calling was performed in parallel using 3 variant callers: GenomeAnalysisTK-2.2-16, Samtools-0.1.18 and MuTect-1.1.4 (McKenna et al., Genome Res, 2010; Li et al., Oxford J, 2009 Aug; Cibulskis et al., Nature, 2013). Annovar-v2012-10-23 with cosmic-v64 and dbsnp-v137 were used for the annotation and RefSeq for the structural annotation. For GATK and Samtools, single nucleotide variants (SNVs) with a quality under 30, a depth of coverage under 6 or with less than 2 reads supporting the variant were filter out. MuTect with parameters following GATK and Samtools thresholds have been used to filter our irrelevant variants. .SNVs within and around exons of coding genes overlapping splice sites.. Then,variants reported in more than 1% of the population in the 1000 genomes (1000gAprl_2012) or Exome Sequencing Project (ESP6500) have been discarded in order to filter polymorphisms. Finally, synonymous variants were filtered out. MuTect focuses on somatic by filtering with constitutional sample. Mpileup comparison between constitutional and somatic DNAs allowed us to focus also on tumor specific SNVs with GATK and Samtools. Finally, every SNV called by our pipeline and also supported in any constitutional samples were filtered our in order to prevent putative constitutional DNA coverage deficiency. Then we analyzed CNVs (copy number variants) with HMMcopy-v0.1.1 (Gavin et al., Genome Res, 2012) and control-FREEC-v6.7 (Boeva et al., Bioinformatics 2011) with a respective window of 2000bp and 1000 bp, and auto-correction of normal contamination of tumor samples for Control-FREEC. Finally we explored Structural variants (SVs) including deletions, inversions, tandem duplications and translocations using DELLY-v0.5.5 with standard parameters (Rausch et al., Oxford J, 2012). In tumors, at least 10 supporting reads were required to make a call and 5 supporting reads for the sample NB0175 with a coverage of only 40X (see table 2). To predict SVs in constitutional samples for subsequent somatic filtering, only 2 supporting reads were required in order not to miss one. To identify somatic events, all the SVs in each normal sample were first flanked by 500 bp in both directions and any SVs called in a tumor sample which was in the combined flanked regions of respective normal sample was removed (see graph 1). Deletions with more than 5 genes impacted or larger than 1Mb and inversions or tandem duplications covering more than 4 genes, were removed. We focused on exonic and splicing events for deletions, inversions, and tandem duplications. For translocation, we keep all SVs that occurred in intronic, exonic, 5'UTR, upstream or splicing regions. Bioinformatics detection of variations with Deep sequencing approach Once PE reads merged and adaptors trimmed by SeqPrep with default parameters, merged reads were aligned via the BWA (Li H. and Durbin R. 2009 PMID 19451168) allowing up to 1 differences in the 22-base-long seeds and reporting only unique alignments. Only reads having a mapping quality 20 or more have been further analysed. Variant calling software was not used, since we aimed to predict variations at low frequencies, observed in less than 1% of reads. Such variants require a custom approach. Using DepthOfCoverage functions of the Genome Analysis Toolkit (GATK) v2.13.2 (McKenna A, et al., 2010 Genome Research PMID: 20644199), we focused on high quality coverage of bases A, C, G and T at the targeted variant position. Depth of coverage of each base following a mapping quality higher than 20 and a base quality higher than 10 have been taken into account in order to focus only on high quality data. Aiming to determine the background level of variability at the studied regions, 10 control samples were included in the analysis. The same approach and filtering criteria have been applied as introduced above over the entire amplicons. In order to highlight variants, for each sample the frequencies of each bases at each amplicon position were then compared to those observed in the set of controls. Statistical analyses were performed with the R statistical software (http://www.R-project.org). Fisher’s exact two-sided tests with a Bonferroni correction were performed to compare percentages of bases between the data sets, i.e. for a given base between a case and the controls. Finally, significant variations were filtered-in once (i) a significant increase in the percentage of avariant base and (ii) a significant decrease in the percentage of it's reference base following our p.values criteria was observed (p.val < 0.05). Illumina HiSeq 2500; 25 bam
EGAD00001002065 Cetuximab is a targeted monoclonal antibody against the epidermal growth factor receptor (EGFR) which is used therapeutically for the treatment of KRAS wild-type colorectal cancer (CRC). The Cetuximab sensitive KRAS wild-type CRC cell line NCI-H508 has been treated with a fixed concentration of ENU for 24 hours and then selected with Cetuximab until drug resistant clones were ready to be picked and grown up as sub-clones of the parental cell line. These will have genes causally implicated in cancer sequenced to identify common point mutations in multiple independently derived drug resistant clones as a forward genetic screen for mechanisms of resistance to Cetuximab in CRC Illumina HiSeq 2500; 50 cram
EGAD00001001375 Samples will be from the BRF113683 (BREAK-3) study which is a Phase III Randomized, Open-label Study Comparing GSK2118436 to Dacarbazine (DTIC) in Previously Untreated Subjects With BRAF Mutation Positive Advanced (Stage III) or Metastatic (Stage IV) Melanoma (n=250 enrolled) *NGS [Agilent capture (Sanger V2 panel): 360 genes and 20 gene fusions; Illumina HiSEQ Sequencing] *CNV: [via NGS or Affy SNP 6.0 or Illumina Omni (TBD)] Bioinformatics: Analysis will be performed using core Sanger informatics pipelines similar to those previously described (Papaemmanuil E et al. (2013) Blood. 22:3616 -3627). Briefly, copy number analysis will be performed using the ASCAT algorithm, and base substitutions, small insertions and deletions using the CAVEMAN and Pindel algorithms, respectively. Statistical approaches including generalized linear models will be used to predict clinical variables such as maximum clinical response and duration of response using genetic data. Sanger and EBI to conduct analysis; Raw data and correlation with clinical endpoints to be analyzed by both EBI/Sanger and GSK (unique pipeline analyses to increase call confidence) Illumina HiSeq 2500; 169 cram
EGAD00001001364 This dataset contains whole exome data from 8 esophageal adenocarcinoma tumors, that has been subjected to multiregion sequencing, ranging from 3-8 regions per tumor. In total, 40 tumor samples and 8 normal blood samples have been sequenced on Illumina HiSeq 2500 at a median dept of 90x. Illumina HiSeq 2500; 47 bam
EGAD00001001389 Genome wide CRISPR screen was performed to find resistance to targeted drugs for melanoma and lung Illumina HiSeq 2500; 15 cram
EGAD00001000992 HIPO blastemal Wilms (nephroblastoma) characterisation of tumor driving events caused by differential SIX1 binding of the SIX1 Q177R mutatns Illumina HiSeq 2500; 3 fastq
EGAD00001001384 Mutations that activate the RAF-MEK-ERK signaling pathway, in particular BRAFV600E, occur in many cancers, and mutant BRAF-selective inhibitors have clinical activity in these diseases. Activating BRAF alleles are usually considered to be mutually exclusive with mutant RAS, whereas inactivating mutations in the D594F595G596 motif of the BRAF activation segment can coexist with oncogenic RAS and cooperate via paradoxical MEK/ERK activation. We determined the functional consequences of a largely uncharacterized BRAF mutation, F595L, which was detected along with an HRASQ61R allele by clinical exome sequencing in a patient with histiocytic sarcoma and also occurs in epithelial cancers, melanoma, and neuroblastoma, and investigated its interaction with mutant RAS. We demonstrate that, unlike previously described DFG motif mutants, BRAFF595L is a gain-of-function variant with intermediate activity towards MEK that does not act paradoxically, but nevertheless cooperates with mutant RAS to promote oncogenic signaling. Of immediate clinical relevance, BRAFF595L shows divergent responses to different mutant BRAF-selective inhibitors, whereas signaling driven by BRAFF595L with and without mutant RAS is efficiently blocked by pan-RAF and MEK inhibitors. Mutation data from primary patient samples and cell lines show that BRAFF595L, as well as other BRAF mutations with intermediate activity, frequently coincide with mutant RAS in a broad spectrum of cancers. These data define a novel class of activating BRAF mutations that cooperate with oncogenic RAS in a non-paradoxical fashion to achieve an optimal level of MEK-ERK signaling, extend the spectrum of patients with systemic histiocytic disorders and other malignancies who are candidates for therapeutic blockade of the RAF-MEK-ERK pathway, and underscore the value of comprehensive genetic profiling for understanding the signaling requirements of individual cancers. Illumina HiSeq 2500; 2 fastq
EGAD00001001598 RNA-sequencing data from teh hT-RPE-MycER cell line after MYC activation and after MINCR knock-down in conditions of MYC ON or OFF Illumina HiSeq 2500; 18 fastq
EGAD00001001668 Data from the paper Context-specific Effects of TGFβ/SMAD3 in Cancer Are Modulated by the Epigenome. Tufegdzic et al, Cell Reports 2015 Illumina HiSeq 2500; 12 bam
EGAD00001001669 Data from the paper Context-specific Effects of TGFβ/SMAD3 in Cancer Are Modulated by the Epigenome. Tufegdzic et al, Cell Reports 2015 Illumina HiSeq 2500; 42 bam
EGAD00001000996 Whole exome sequencing data for AML and matched normal samples Illumina HiSeq 2500; 16 bam
EGAD00001001688 Illumina HiSeq 2500; 34 fastq
EGAD00001001689 Illumina HiSeq 2500; 27 fastq
EGAD00001001686 In the autozygosity exome sequencing of Born-in-Bradford samples of Pakistani origin there is a mother who is homozygous for an apparent truncating stop codon in PRDM9, the gene responsible for localising recombination during meiosis. We plan to deep sequence mother and child with X10, and physically phase the mother with PacBio sequencing. We will use this data to identify recombination locations, and test whether these are consistent with the known fine scale recombination map. Data Access is controlled by the Wellcome Trust Sanger Institute DAC and the Born In Bradford Executive Group. Illumina HiSeq 2500; 2 cram
EGAD00001002161 Transcriptome from EGAS00001001845 Illumina HiSeq 2500; 1 fastq
EGAD00001002160 Exome Seq for EGAS00001001845 Illumina HiSeq 2500; 2 fastq
EGAD00001002162 Exome Seq from EGAS00001001846 Illumina HiSeq 2500; 2 fastq
EGAD00001001909 Paired-end whole exome sequenncing (Illumina) of primary enucleated retinoblastoma and matching lymphocyte DNA was performed to find somatic alterations that are related to oncogenesis. Illumina HiSeq 2500; 143 fastq
EGAD00001001921 All pituitary samples Illumina HiSeq 2500; 84 bam
EGAD00001001920 TEST3 dataset containing 1 FASTQ file with mRNA reads. Illumina HiSeq 2500; 1 fastq
EGAD00001001938 DNA from each sample (100ng) was sheared on Covaris S220 (Covaris): duty cycle - 10%, intensity -5.0, bursts per sec - 200, duration - 300 sec, mode - frequency sweeping, power - 23V, temperature -5:5 ?C to 6 ?C, water level - 13. Libraries were prepared with the TruSeq Nano DNA LT Sample Prep Kit (Illumina) using a modi?ed protocol - Sample Puri?cation Beads were replaced by Agencourt AMPure XP beads (Beckman Coultier) and size selection after the End Repair was done to remove only the short fragments. Quality and quantity for contructed libraries were assessed with DNA 7500 kit on Agilent 2100 Bioanalyzer and with Kapa Quanti?cation kit (KAPA Biosystems) on 7900HT Fast Real-Time PCR System (Applied Biosystems) according to the supplier's recommendations, respectively. Libraries from 18 barcoded samples were pooled together in equimolar amounts and each pool was loaded on a single lane of a HiSeq Single End Flowcell (Illumina), followed by cluster generation on a cBot (Illumina) and sequencing on a HiSeq 2500 (Illumina) in a single-read 50bp mode. Reads were aligned using bwa-mem v0.7.12-r1039 [10] to the 1000 genomes version of human genome build GRCh37. Picard (http://picard.sourceforge.net) was used to remove duplicate reads. Illumina HiSeq 2500; 60 bam
EGAD00001001984 To identify recurrent somatic alterations in this unique subset of gastric cancers, whole exome and SNP6 analyses were performed using frozen cancer tissue. The somatic mutation analyses were also performed using blood of the same patients. Illumina HiSeq 2500; 160 bam
EGAD00001001986 This study is meant to gain further knowledge in haematological cancers. Patients samples (mainly DNAs or PCR products) from haematolocical cancer patients will be sequenced, and the outputs will be correlated to their diagnosis and/or prognosis; the findings may also add more insight into the understanding of biology in this type of tumour. We will be sequencing Primary Testicular Lymphomas (PTL) to identify genetic drivers of this rare cancer Illumina HiSeq 2500; 7 cram
EGAD00001001957 March 2016 update of Whole genome bisulfite sequencing assay data (fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2500; 18 fastq
EGAD00001002064 Zhong Shan Hospital liver tumor single cell sequencing: 111 single cell and 6 tissues Illumina HiSeq 2500; 117 fastq
EGAD00001002051 BRAF V600E colorectal cancers do not respond to the only currently FDA approved targeted therapy for CRC. There is currently a trial underway in the UK recruiting V600E CRC patients for treatment with a triple therapy combination of Cetuximab, Trametinib and Dabrafenib. We have mutagenized a pool of V600E CRC cell lines and treated with this triple therapy to select out drug resistant clones. We will now sequence these drug resistant clones with the aim of identifying common point mutations engendering resistance to this new therapy. Illumina HiSeq 2500; 20 cram
EGAD00001002066 KRAS mutant CRC is currently in clinical trial with a combination of a MEK and Akt inhibitor. These patients will likely develop resistance to this combination. We aim to identify the mechanisms of resistance via ENU mutagenesis, with a view to identifying additional therapeutics which have the ability to overcome this resistance. Illumina HiSeq 2500; 86 cram
EGAD00001002187 To identify transcriptome profile in this unique subset of gastric cancers, RNA-seq analyses were performed using frozen cancer tissue. Adjacent normal tissue of the same patients were used in differently expressed gene selection and fusion gene prediction. Illumina HiSeq 2500; 138 bam
EGAD00001002111 70 Whole exome sequencing from 9 patients with DIPG for project Spatial and Temporal Homogeneity of Driver Mutations in Diffuse Intrinsic Pointine Glioma Illumina HiSeq 2500; 70 bam
EGAD00001002226 1. Odors are detected, firstly, by olfactory sensory neurons (OSNs) in the olfactory epithelium of the nose. This neurons then project directly to the olfactory bulb in the brain. Olfaction depends on cellular regeneration of the OE, olfactory bulb and hippocampus, and on their continual re-wiring. The olfactory neural pathway includes regions of the frontal, temporal and limbic brain, which in turn overlap with brain areas involved in brain disorders. OSNs are the only aspect of the human brain exposed to the external environment. This not only makes them vulnerable to environmental changes, but also accessible for biomedical studies. We have already sequenced and developed a protocol for analyzing the transcriptome of mouse main olfactory epithelium and single OSNs. We propose here to perform a similar study for samples from the human olfactory epithelium. We have developed a minimally invasive method for obtaining human OSNs, among other cells from the nasal epithelium. In this experiment, we have obtained cell samples from the olfactory epithelium, including OSN, from healthy volunteers. We would like to further characterize them by RNA sequencing. This will give us valuable insight into human olfaction. It will also provide a first step into a new avenue to study, and find biomarkers for, brain diseases though the analysis of these easily available neurons. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina HiSeq 2500; 8 cram
EGAD00001002143 We expanded our previous collection of longitudinal GBM patients (EGAS00001001041) by recruiting 21 additional patients. Tumor specimens were subjected to whole-exome sequencing (16 of 21 cases, with the matched normal/blood) and transcriptome sequencing (16 of 21 cases). Illumina HiSeq 2500; 86 fastq
EGAD00001001923 RNA sequence data for conditionally reprogrammed cells from patient HUB_5 Illumina HiSeq 2500; 1 fastq
EGAD00001002197 Recent GWAS studies have made extensive use of large eQTL data sets to functionally annotate index SNPs. With a large number of association signals located outside coding regions there has been an intense search among sequence variants affecting gene expression at the transcriptional level. However, little progress has been made in mapping regulatory variants that affect protein levels at the translational or post-translational level. It is now possible to undertake a protein QTL scan for focused sets of e.g. oxidized proteins by mass spectrometry. We have established a collaboration with a longitudinal, family-based study in France, the Stanislas cohort, which comprises circa 1000 nuclear families (4,295 individuals) and has follow up data for 10 years (three visits). We have undertaken a pilot study in a focus set of 257 subjects from 79 families with the aim to integrate GWAS, transcriptomic and DNA methylation data with proteomic data on a set of 100 proteins measured in PBMCs. We have already generated GWAS data using Illumina's core-exome chip as well as DNA methylation profiles with the 450K array. We propose to use RNA seq to generate transcriptomic data of the corresponding PBMCs. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina HiSeq 2500; 155 cram
EGAD00001002204 1006 Familial early onset gemrline CRC patients sequenced by the Molecular and Population Genetics group of the Institute of Cancer Research Illumina HiSeq 2500; 1,006 bam
EGAD00001002188 Paired-end BAM files of mitochondrial whole genome deep sequencing (mtWGDS) analysis Illumina HiSeq 2500; 105 bam
EGAD00001002163 Transcriptome from EGAS00001001846 Illumina HiSeq 2500; 1 fastq
EGAD00001002243 RNA-seq data for patient samples Illumina HiSeq 2500; 2 fastq
EGAD00001002244 WGS data for cell lines and patient samples Illumina HiSeq 2500; 4 fastq
EGAD00001002145 Whole exome sequencing data of primary, secondary and tertiary tumor from a patient. Illumina HiSeq 2500; 4 fastq
EGAD00001002006 Whole genome sequencing of paediatric glioblastoma in the ICGC PedBrain project Illumina HiSeq 2500; 115 fastq
EGAD00001001944 RNA sequencing of paediatric glioblastoma in the ICGC PedBrain project Illumina HiSeq 2500; 42 fastq
EGAD00001002067 Renal cell carcinoma (RCC) is a genomically heterogeneous tumor. In the present project, the question whether intratumoral heterogeneity follows a zonal pattern indicating spatial niches was addressed. Whole exome sequencing of 16 paired samples from tumor periphery and center revealed a number of region-specific functional SNVs and Indels. Therefore, RCCs are not composed of evenly admixed tumor cells but show topological differences in their clonal composition. Illumina HiSeq 2500; 16 fastq
EGAD00001002253 Thirty cutaneous SCC WES tumour samples with matched normal include 20 samples from South et al. JID and 10 new samples. These 30 samples has been used to support the findings in the TGFb Nature Communications paper (DOI: 10.1038/ncomms12493). They are also a part of the ongoing study of cSCC genomic landscape of 40 cSCC samples in total. Illumina HiSeq 2500; 60 bam
EGAD00001002270 We collected fresh tissue from an untreated GBM (SF10282) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells. Illumina HiSeq 2500; 1 fastq
EGAD00001002203 Sequence data is from 4 samples from an adult patient with TCF3-PBX1 t(1;19)-positive acute lymphoblastic leukemia. Exome sequencing was performed on a skin biopsy (normal tissue control) and leukemic bone marrow biopsies taken at diagnosis and at two relapse time points. RNA-sequence data is from leukemic bone marrow from two relapse biopsies. Illumina HiSeq 2500; 4 fastq,bam
EGAD00001001913 Exome sequencing data for Mesothelioma Illumina HiSeq 2500; 198 fastq
EGAD00001002249 Single-Cell RNA Sequencing of 355 cells isolated from 7 tissue fragments of 3 patients corresponding to locally adjacent tumor, multifocal with recurrence and sections segregated by a marker of tumor cellularity (5-ALA). Illumina HiSeq 2500; 355
EGAD00001001468 PAR-CLIP was performed on the Argonaute-2 protein (AGO2) in four lymphoma cell lines: Namalwa Raji SU-DHL-4 SU-DHL-6 Illumina HiSeq 2500; 4 fastq
EGAD00001001612 After overexpression and knockdown of both described novel miRs nmiR-1 and nmiR-2 in BL cell lines (SU-DHL4 for nmiR-1 and Raji for nmiR-2), we performed regular RNA-Seq (including Mock controls for all cell lines) to identify their direct and indirect downstream mRNA targets. Illumina HiSeq 2500; 16 fastq
EGAD00001002736 WES of human: A mutation in VPS15 (PIK3R4) causes a ciliopathy and affects IFT20 release from the cis-Golgi WES (Agilent SureSelect All Exon XT2 50 Mb kit) has been realized on three affected siblings (II.1, II.3, II.5) and one healthy sister (II.4). Raw data (BAM files) are provided: - II.1.aligned.sorted.dedup.realign.recal.bam - II.3.aligned.sorted.dedup.realign.recal.bam - II.5.aligned.sorted.dedup.realign.recal.bam - II.4.aligned.sorted.dedup.realign.recal.bam Illumina HiSeq 2500; 4 bam
EGAD00001002262 26 cell lines derived from human Diffuse Large B Cell lymphomas (DLBCL) or Burkit Lymphomas (BL) were subjected to whole exome sequencing. Exome capture was carried out using the SeqCap EZ Exome Library 2.0 kit (Roche/Nimblegen) and 100 bp single-read sequencing was performed on a HiSeq2500 (Illumina). 82% of the coding region was covered at least 30x. Illumina HiSeq 2500; 26 bam
EGAD00001002248 Total of 49 tumor specimens from 20 patients were subjected for whole-exome and/or whole-transcriptome sequencing including matched normal/blood. Tumor samples are acquired based on 4 categories; 1) locally adjacent tumors, 2) multifocal/multicentric tumors, 3) 5-ALA (+/-) tumors and 4) Longitudinal tumors. Illumina HiSeq 2500; 104
EGAD00001001374 The mtDNA and Y chromosome of up to 15 Australian Aborigines, concentrating on individuals with indigenous lineages will be sequenced using the standard whole-genome sequencing followed by filtering out autosomal and X sequences, so that only mtDNA and the Y chromosome would be analysed and released. Illumina HiSeq 2500; 6
EGAD00001001994 CCA targeted sequencing Illumina HiSeq 2500; 376
EGAD00001001980 This dataset contains BAM files of targeted Amplicon deep-sequencing data, for validation of the mutations found in WES. There are 16 patients and 95 samples in total, including 16 controls and 79 tumors. Illumina HiSeq 2500; 95
EGAD00001001981 This dataset contains FASTQ files of targeted Amplicon deep-sequencing data, for validation of the mutations found in WES. There are 16 patients and 95 samples in total, including 16 controls and 79 tumors. 140 fastq in total, multiple runs for some of the samples. Please refer to the sample-ID from filename for merging. Illumina HiSeq 2500; 95
EGAD00001003337 T cells isolated from peripheral blood, tumors and adjacent normal tissues from six hepatocellular carcinoma patients. SmartSeq2 and Tang2009 protocol were used to amplify RNA from single T cells. High depth enables simultaneously expression profiling and TCR assembling. Illumina HiSeq 2500 (ILLUMINA), Illumina HiSeq 4000 (ILLUMINA) 5,063
EGAD00001003523 HipSci - Hypertrophic Cardiomyopathy - Exome Sequencing - July 2017 Illumina HiSeq 2500 (ILLUMINA), Illumina HiSeq 2500;ILLUMINA 18
EGAD00001003528 HipSci - Usher Syndrome - Exome Sequencing - July 2017 Illumina HiSeq 2500 (ILLUMINA), Illumina HiSeq 2500;ILLUMINA 27
EGAD00001003394 This dataset contains bam files for ChIP-seq experiments for 6 neuroblastoma PDXs (Patient Derived Xenograft). It includes the bam files for the H3K27ac mark as well as the bam files of the corresponding input DNA for each sample. Illumina HiSeq 2500 (ILLUMINA) 6
EGAD00001003194 This dataset contains whole exome sequence of six HCC patients from Qidong China who are very likely exposed to aflatoxin. Illumina HiSeq 2500 (ILLUMINA) 12
EGAD00001003516 HipSci - Monogenic Diabetes - Exome Sequencing - July 2017 Illumina HiSeq 2500 (ILLUMINA) 43
EGAD00001003517 HipSci - Alport Syndrome - Exome Sequencing - July 2017 Illumina HiSeq 2500 (ILLUMINA) 7
EGAD00001003518 HipSci - Battens Disease - Exome Sequencing - July 2017 Illumina HiSeq 2500 (ILLUMINA) 4
EGAD00001003519 HipSci - Bleeding and Platelet Disorders - Exome Sequencing - July 2017 Illumina HiSeq 2500 (ILLUMINA) 7
EGAD00001003520 HipSci - Congenital Hyperinsulinia - Exome Sequencing - July 2017 Illumina HiSeq 2500 (ILLUMINA) 5
EGAD00001003521 HipSci - Hereditary Cerebellar Ataxias - Exome Sequencing - July 2017 Illumina HiSeq 2500 (ILLUMINA) 11
EGAD00001003522 HipSci - Hereditary Spastic Paraplegia - Exome Sequencing - July 2017 Illumina HiSeq 2500 (ILLUMINA) 6
EGAD00001003525 HipSci - Macular Dystrophy - Exome Sequencing - July 2017 Illumina HiSeq 2500 (ILLUMINA) 3
EGAD00001003524 HipSci - Kabuki Syndrome - Exome Sequencing - July 2017 Illumina HiSeq 2500 (ILLUMINA) 6
EGAD00001003526 HipSci - Primary Immune Deficiency - Exome Sequencing - July 2017 Illumina HiSeq 2500 (ILLUMINA) 8
EGAD00001003527 HipSci - Retinitis Pigmentosa - Exome Sequencing - July 2017 Illumina HiSeq 2500 (ILLUMINA) 2
EGAD00001003529 HipSci - Healthy Normals - RNA Sequencing - July 2017 Illumina HiSeq 2500 (ILLUMINA) 193
EGAD00001003530 HipSci - Monogenic Diabetes - RNA Sequencing - July 2017 Illumina HiSeq 2500 (ILLUMINA) 43
EGAD00001003531 HipSci - Bardet-Biedl Syndrome - RNA Sequencing - July 2017 Illumina HiSeq 2500 (ILLUMINA) 59
EGAD00001003532 HipSci - Alport Syndrome - RNA Sequencing - July 2017 Illumina HiSeq 2500 (ILLUMINA) 7
EGAD00001003534 HipSci - Congenital Hyperinsulinia - RNA Sequencing - July 2017 Illumina HiSeq 2500 (ILLUMINA) 5
EGAD00001003535 HipSci - Kabuki Syndrome - RNA Sequencing - July 2017 Illumina HiSeq 2500 (ILLUMINA) 6
EGAD00001003536 HipSci - Primary Immune Deficiency - RNA Sequencing - July 2017 Illumina HiSeq 2500 (ILLUMINA) 8
EGAD00001003537 HipSci - Hereditary Spastic Paraplegia - RNA Sequencing - July 2017 Illumina HiSeq 2500 (ILLUMINA) 6
EGAD00001003538 HipSci - Hereditary Cerebellar Ataxias - RNA Sequencing - July 2017 Illumina HiSeq 2500 (ILLUMINA) 11
EGAD00001003539 HipSci - Bleeding and Platelet Disorders - RNA Sequencing - July 2017 Illumina HiSeq 2500 (ILLUMINA) 7
EGAD00001003540 HipSci - Hypertrophic Cardiomyopathy - RNA Sequencing - July 2017 Illumina HiSeq 2500 (ILLUMINA) 18
EGAD00001003541 HipSci - Macular Dystrophy - RNA Sequencing - July 2017 Illumina HiSeq 2500 (ILLUMINA) 3
EGAD00001003542 HipSci - Retinitis Pigmentosa - RNA Sequencing - July 2017 Illumina HiSeq 2500 (ILLUMINA) 2
EGAD00001003543 HipSci - Usher Syndrome - RNA Sequencing - July 2017 Illumina HiSeq 2500 (ILLUMINA) 27
EGAD00001002297 ChIP-Seq data for 2 monocyte - RPMI_BG_T=1hr sample(s). 6 run(s), 6 experiment(s), 6 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA, unspecified;ILLUMINA 2 bam,fastq
EGAD00001002388 ChIP-Seq data for 3 monocyte - RPMI_LPS_T=24hrs sample(s). 8 run(s), 8 experiment(s), 8 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA, unspecified;ILLUMINA 3 bam,fastq
EGAD00001002368 ChIP-Seq data for 3 monocyte - RPMI_BG_T=4hrs sample(s). 8 run(s), 8 experiment(s), 8 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA, unspecified;ILLUMINA 3 bam,fastq
EGAD00001002415 ChIP-Seq data for 3 monocyte - Attached_T=1hr sample(s). 8 run(s), 7 experiment(s), 7 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA, unspecified;ILLUMINA 3 bam,fastq
EGAD00001002376 ChIP-Seq data for 2 monocyte - RPMI_LPS_T=1hr sample(s). 8 run(s), 6 experiment(s), 6 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA, unspecified;ILLUMINA 2 bam,fastq
EGAD00001002390 ChIP-Seq data for 4 segmented neutrophil of bone marrow sample(s). 24 run(s), 23 experiment(s), 23 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA, NextSeq 500;ILLUMINA 4 bam,fastq
EGAD00001002314 ChIP-Seq data for 2 macrophage - T=6days B-glucan sample(s). 6 run(s), 6 experiment(s), 6 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA, NextSeq 500;ILLUMINA 2 bam,fastq
EGAD00001003428 RNAseq data from the study: "Widespread DNA hypomethylation and differential gene expression in Turner syndrome". Illumina HiSeq 2000;ILLUMINA, NextSeq 500;ILLUMINA 37
EGAD00001003705 10 single-cell placental RNA libraries were generated using the Chromium Single Cell 3′ Reagent Kit (10X Genomics). All single-cell libraries were sequenced with a customized paired end with dual indexing (98/14/8/10-bp) format according to the recommendation by 10X Genomics. The data were aligned using the Cell Ranger Single-Cell Software Suite (version 1.0). Moreover, plasma RNA from 22 samples were extracted using the RNeasy Mini Kit (Qiagen). cDNA reverse transcription, second-strand synthesis, and RNA-sequencing (RNA-seq) library construction were performed using the Ovation RNA-seq System V2 (NuGEN) kit according to the manufacturer’s protocol. For alignment of the plasma RNA library, adaptor sequences and low-quality bases on the fragment ends (i.e., quality score < 5) were trimmed, and reads were aligned to the human reference genome (hg19) using the TopHat (v2.0.4) software. All aligned reads were deposited in bam file format. Illumina HiSeq 2000;ILLUMINA, NextSeq 500;ILLUMINA 32
EGAD00001003761 This dataset contains fastq files with Whole genome sequencing data for the CPC-Gene Project. Data from each sample was generated using multiple whole genome libraries and sequenced across multiple runs Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA, unspecified;ILLUMINA 617
EGAD00001003706 This dataset contains fastq files with Whole genome sequencing data for the CPC-Gene Project. Data from each sample was generated using multiple whole genome libraries and sequenced across multiple runs Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA, unspecified;ILLUMINA 616
EGAD00001001400 Fastq data for whole genome shotgun sequencing assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 27 fastq
EGAD00001001405 Fastq data for ChIP-Seq (H3K36me3) assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 48 fastq
EGAD00001001404 Fastq data for ChIP-Seq (H3K27me3) assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 48 fastq
EGAD00001001402 Fastq data for stranded mRNA-Seq assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 32 fastq
EGAD00001001403 Fastq data for ChIP-Seq (H3K27ac) assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 48 fastq
EGAD00001001406 Fastq data for ChIP-Seq (H3K4me1) assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 48 fastq
EGAD00001001407 Fastq data for ChIP-Seq (H3K4me3) assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 48 fastq
EGAD00001001408 Fastq data for ChIP-Seq (H3K9me3) assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 48 fastq
EGAD00001001409 Fastq data for ChIP-Seq (Input) assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 48 fastq
EGAD00001002527 DEEP (German Epigenome Project) sequence data of following samples (Sequencing Types: Chip-Seq, WGBS-Seq, RNA-Seq, sncRNA-Seq, NOMe-Se, DNase-Seq): 41_Hf01_LiHe_Ct, 41_Hf02_LiHe_Ct, 41_Hf03_LiHe_Ct, 01_HepG2_LiHG_Ct1, 01_HepG2_LiHG_Ct2, 01_HepaRG_LiHR_D31, 01_HepaRG_LiHR_D32, 01_HepaRG_LiHR_D33, 43_Hm01_BlMo_Ct, 43_Hm03_BlMo_Ct, 43_Hm05_BlMo_Ct, 43_Hm03_BlMa_Ct, 43_Hm05_BlMa_Ct, 43_Hm03_BlMa_TO, 43_Hm05_BlMa_TO, 43_Hm03_BlMa_TE, 43_Hm05_BlMa_TE, 51_Hf01_BlCM_Ct, 51_Hf03_BlCM_Ct, 51_Hf04_BlCM_Ct, 51_Hf02_BlCM_Ct, 51_Hf05_BlCM_Ct, 51_Hf06_BlCM_Ct, 51_Hf06_BlCM_T1, 51_Hf06_BlCM_T2, 51_Hf03_BlEM_Ct, 51_Hf04_BlEM_Ct, 51_Hf02_BlEM_Ct, 51_Hf05_BlEM_Ct, 51_Hf06_BlEM_Ct, 51_Hf06_BlEM_T1, 51_Hf06_BlEM_T2, 51_Hf03_BlTN_Ct, 51_Hf04_BlTN_Ct, 51_Hf02_BlTN_Ct, 51_Hf05_BlTN_Ct, 51_Hf06_BlTN_Ct, 51_Hf06_BlTN_T1, 51_Hf06_BlTN_T2, 51_Hf07_BmTM4_Ct, 51_Hf08_BlTM4_Ct, 51_Hf08_BmTM4_SP1, 51_Hf08_BmTM4_SP2, 51_Hf05_BlTA_Ct, 44_Mm01_WEAd_C2, 44_Mm03_WEAd_C2, 44_Mm02_WEAd_C2, 44_Mm07_WEAd_C2, 44_Mm04_WEAd_C1, 44_Mm05_WEAd_C1 Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 50 fastq
EGAD00001002671 RNA-Seq data for 212 CD4-positive, alpha-beta T cell sample(s). 212 run(s), 212 experiment(s), 212 analysis(s) on human genome GRCh37. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/blueprint_Epivar/protocols/README_rnaseq_analysis_sanger_20160816 Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 212 bam,fastq
EGAD00001002673 ChIP-Seq data for 154 CD4-positive, alpha-beta T cell sample(s). 355 run(s), 265 experiment(s), 250 analysis(s) on human genome GRCh37. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/blueprint_Epivar/protocols/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 158 bam,fastq
EGAD00001002670 ChIP-Seq data for 182 mature neutrophil sample(s). 2847 run(s), 366 experiment(s), 355 analysis(s) on human genome GRCh37. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/blueprint_Epivar/protocols/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 186 fastq,cram,bam
EGAD00001002672 ChIP-Seq data for 172 CD14-positive, CD16-negative classical monocyte sample(s). 572 run(s), 345 experiment(s), 340 analysis(s) on human genome GRCh37. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/blueprint_Epivar/protocols/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 174 bam,fastq
EGAD00001002675 RNA-Seq data for 205 mature neutrophil sample(s). 205 run(s), 205 experiment(s), 205 analysis(s) on human genome GRCh37. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/blueprint_Epivar/protocols/README_rnaseq_analysis_sanger_20160816 Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 205 bam,fastq
EGAD00001002674 RNA-Seq data for 197 CD14-positive, CD16-negative classical monocyte sample(s). 197 run(s), 197 experiment(s), 197 analysis(s) on human genome GRCh37. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/blueprint_Epivar/protocols/README_rnaseq_analysis_sanger_20160816 Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 197 bam,fastq
EGAD00001002745 Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 7 fastq
EGAD00001003153 Sequencing of untreated pancreatic cancer metastases and primary tumor sections. Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 49
EGAD00001002735 mRNA, total RNA, small noncoding RNA, NOMe-Seq and DNase-Seq data from following samples (not every Sequencing Type for every sample): 01_HepG2_LiHG_Ct1 41_Hf01_LiHe_Ct 41_Hf02_LiHe_Ct 41_Hf03_LiHe_Ct 51_Hf03_BlCM_Ct 51_Hf04_BlCM_Ct 51_Hf03_BlEM_Ct 51_Hf04_BlEM_Ct 51_Hf03_BlTN_Ct 51_Hf04_BlTN_Ct Metadata available at deep.dkfz.de Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 10
EGAD00001003181 HipSci - Bardet-Biedl Syndrome - RNA Sequencing - October 2016 Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 37
EGAD00001003180 HipSci - Monogenic Diabetes - RNA Sequencing - October 2016 Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 35
EGAD00001003215 This data set contains whole exome sequences of individuals with self-stated parental relatedness from the East London Genes & Health cohort. Rare frequency functional variants in these healthy individuals will be studied with respect to the genetic health of the participants and loss-of-function analysis of human genes. Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 1,702
EGAD00001003329 The offspring of first cousin marriages have ~6% of their genome autozygous, i.e. homozygous identical by descent, or even more if there was further consanguinity in their ancestry. In the UK there are large populations with very high first cousin marriage rates of 20-50%. Sequencing the exomes of a sample of these individuals has the potential both to support genetic health programmes in these populations, and to provide genetic research information about rare loss of function mutations. This pilot study based on existing cohort samples from the Born In Bradford study will identify homozygous individuals for almost all variants down to an allele frequency around 1%, plus individuals carrying hundreds of new homozygous rare loss-of-function variants, and will support development of community relations and ethics for a wider study currently being designed. The data deposited in the EGA consist of low coverage whole exome sequencing on these samples. This dataset contains all the data available for this study on 2017-05-11. Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 3,188
EGAD00001003320 Transcriptome sequencing of tumour tissue, adjacent normal tissue and derived organoids/tumoroids from colorectal cancer This dataset contains all the data available for this study on 2017-05-04. Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 106
EGAD00001003331 Whole-exome sequencing of a cohort of families (probands and affected/unaffected relatives) suffering from one of two rare thyroid disorders: congenital hypothyroidism (CH) and resistance to thyroid hormone (RTH). This dataset contains all the data available for this study on 2017-05-11. Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 78
EGAD00001003276 Whole genome sequencing data for MMML (24 tumor/control pairs), fastq-files Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 49
EGAD00001001433 PCGP Germline Study Whole Exome Sequencing Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2000; 906 bam
EGAD00001001432 PCGP Germline Study Whole Genome Sequencing Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2000; 1,337 bam
EGAD00001002395 Bisulfite-Seq data for 2 monocyte - None sample(s). 70 run(s), 4 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2000; 2 bcf,bam
EGAD00001002311 Bisulfite-Seq data for 2 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 29 run(s), 2 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2000; 2 bcf,bam
EGAD00001002419 Bisulfite-Seq data for 19 Acute Myeloid Leukemia sample(s). 338 run(s), 32 experiment(s), 38 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2000; 19 bcf,bam
EGAD00001002367 Bisulfite-Seq data for 2 effector memory CD4-positive, alpha-beta T cell sample(s). 34 run(s), 3 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2000; 2 bcf,bam
EGAD00001002655 BLUEPRINT ChIP-Seq from two mantle cell lymphoma patients Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2000; 2 fastq
EGAD00001002651 Presurgical studies allow study of the relationship between mutations and response of estrogen receptor positive (ER+) breast cancer to aromatase inhibitors (AIs) but have been limited to small biopsies. Here in Phase I of this study, we perform exome sequencing on baseline, surgical core-cuts and blood from 60 patients (40 AI treated, 20 Controls). In poor responders (based on Ki67 change) we find significantly more somatic mutations than good responders. Subclones exclusive to baseline or surgical cores   occur in approximately 30% of tumours. In Phase II we combine targeted sequencing on another 28 treated patients with Phase I. We find six genes frequently mutated: PIK3CA, TP53, CDH1, MLL3, ABCA13 and FLG with 71% concordance between paired cores. TP53 mutations are associated with poor response. We conclude that multiple biopsies are essential for confident mutational profiling of ER+ breast cancer and TP53 mutations are associated with resistance to oestrogen deprivation therapy. Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2000; 443 bam
EGAD00001000082 20 Matched Pair Breast Cancer Genomes Illumina HiSeq 2000;ILLUMINA, Illumina Genome Analyzer II;ILLUMINA 42 bam
EGAD00001001335 We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. Illumina HiSeq 2000;ILLUMINA, Illumina Genome Analyzer II;ILLUMINA 28 bam,srf,cram
EGAD00001001338 We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. Illumina HiSeq 2000;ILLUMINA, Illumina Genome Analyzer II;ILLUMINA 49 bam,srf
EGAD00001002237 The disordered transcriptomes of cancer encompass direct effects of somatic mutation on transcription; co-ordinated secondary alterations in transcriptional pathways; and increased transcriptional noise. To catalogue the rules governing how somatic mutation Overall, 59% of 6980 exonic substitutions were expressed. Compared to other classes, nonsense mutations showed lower expression levels than expected with patterns characteristic of nonsense-mediated decay. 14% of 4234 genomic rearrangements caused transcriptional abnormalities, including exon skips, exon reusage, fusion transcripts and premature poly-adenylation. We found productive, stable transcription from sense-to-antisense gene fusions and gene-to-intergenic rearrangements, suggesting that these mutation classes may drive more transcriptional disruption than previously suspected. Systematic integration of transcriptome with genome data therefore reveals the rules by which transcriptional machinery interprets somatic mutation. Illumina HiSeq 2000;ILLUMINA, Illumina Genome Analyzer II;ILLUMINA 59 bam,srf
EGAD00001003265 For CCOC cohorts, OvCaRe cases were reviewed, including frozen material, by at least two expert gynecopathologists prior to inclusion in the sequencing cohort who provided the confirmation on final selected cohort. Frozen H&E from Tokyo were also used for evaluation along with representative H&E photos and review done at the Jikei School of Medicine. All CCOC tumours are primary tumour samples. Library construction and sequencing Frozen specimens with >50% tumour cellularity (based on initial slide review) were used for cryosectioning and subsequent nucleic acid extraction. Patient tumour and normal blood samples derived from primary, untreated fresh frozen tumour specimens harvested at diagnosis during standard of care debulking surgery. Germline DNA was provided from peripheral blood buffy coat on all specimens except 13 from Tokyo, where non-cancer frozen tissue was used as a germline source. DNA extraction from both matched normal (blood) and tumour samples (frozen tissue) were performed using the QIAamp Blood and Tissue DNA kit (Qiagen) and quantified using a Qbit fluorometer and reagents (high-sensitivity assay). Three lanes of Illumina HiSeq 2500 v4 chemistry for normal samples and five lanes for tumour samples were obtained. The PCR-free protocol was adopted to eliminate the PCR-induced bias and improve coverage across the genome. Illumina HiSeq 2000;ILLUMINA, Illumina Genome Analyzer II;ILLUMINA 70
EGAD00001002656 Whole exome sequencing BAM files and whole genome sequencing CRAM files for 722 individuals from the NIHR-BioResource Rare Diseases Consortium (SPEED project) with inherited retinal disease. Illumina HiSeq 2000;ILLUMINA 767
EGAD00001000265 This Study uses a focused bespoke bait pull down library method to target findings of Chondrosarcoma whole genome and whole exome sequencing studies in order to validate findings. This method will also be used on a larger set of tumour only samples in order to find precedence of these findings in a larger set of patient samples. Illumina HiSeq 2000;ILLUMINA 190
EGAD00001003419 Illumina HiSeq 2000;ILLUMINA 50
EGAD00001001229 ChIP-Seq (H3K27ac) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2000;ILLUMINA 48 bam
EGAD00001001230 ChIP-Seq (H3K27me3) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2000;ILLUMINA 48 bam
EGAD00001001231 ChIP-Seq (H3K36me3) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2000;ILLUMINA 48 bam
EGAD00001001233 ChIP-Seq (H3K4me3) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2000;ILLUMINA 48 bam
EGAD00001001232 ChIP-Seq (H3K4me1) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2000;ILLUMINA 48 bam
EGAD00001001234 ChIP-Seq (H3K9me3) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2000;ILLUMINA 48 bam
EGAD00001001401 Fastq data for smRNA-Seq assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2000;ILLUMINA 28 fastq
EGAD00001001473 Bisulfite-Seq data for 2 cytotoxic CD56-dim natural killer cell sample(s). 24 run(s), 2 experiment(s), 2 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820 Illumina HiSeq 2000;ILLUMINA 2 bam
EGAD00001002755 A KNIH007 Whole-Genome Bisulfite Sequencing(WGBS) paired end data for adipocytes Illumina HiSeq 2000;ILLUMINA 1 fastq
EGAD00001000440 UK10K_NEURO_GURLING REL-2013-04-20 Illumina HiSeq 2000;ILLUMINA 46 bam,vcf
EGAD00001001933 HipSci - Healthy Normals - RNA Sequencing - January 2016 Illumina HiSeq 2000;ILLUMINA 181 other,cram,bai,bam
EGAD00001002757 A KNIH009 Whole-Genome Bisulfite Sequencing(WGBS) paired end data for preadipocytes Illumina HiSeq 2000;ILLUMINA 1 fastq
EGAD00001003349 ChIP-seq data (H3K4Me1, H3K4Me3, H3K27Ac histone modifications) in experimental triplicates on multiple myeloma cell line KMS11 and plasma cell leukaemia cell lines L363 and JJN3. ChIP reactions were performed on a Diagenode SX-8G IP-Star Compact using Diagenode automated Ideal Kit. ChIP libraries were generated using HTP Illumina library preparation kit, and sequenced using Illumina HiSeq 2000 with 100 bp single-ended reads. ChIP-seq files are in BED format. Illumina HiSeq 2000;ILLUMINA 9
EGAD00001001336 We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. Illumina HiSeq 2000;ILLUMINA 6 bam
EGAD00001003154 RNA-Seq files for SJOS study Illumina HiSeq 2000;ILLUMINA 14
EGAD00001003099 RNAseq data set (Mollaoglu et al., MYC drives progression of small cell lung cancer to a variant neuroendocrine subtype with vulnerability to Aurora kinase inhibition) Illumina HiSeq 2000;ILLUMINA 14
EGAD00001002177 A KNIH011 mRNA-seq paired end data for podocytes Illumina HiSeq 2000;ILLUMINA 1 fastq
EGAD00001002176 A KNIH010 mRNA-seq paired end data for podocytes Illumina HiSeq 2000;ILLUMINA 1 fastq
EGAD00001002172 A KNIH006 mRNA-seq paired end data for beta cells Illumina HiSeq 2000;ILLUMINA 1 fastq
EGAD00001002167 A KNIH001 mRNA-seq paired end data for islet cells Illumina HiSeq 2000;ILLUMINA 1 fastq
EGAD00001002174 A KNIH008 mRNA-seq paired end data for adipocytes Illumina HiSeq 2000;ILLUMINA 1 fastq
EGAD00001002168 A KNIH002 mRNA-seq paired end data for islet cells Illumina HiSeq 2000;ILLUMINA 1 fastq
EGAD00001002175 A KNIH009 mRNA-seq paired end data for preadipocytes Illumina HiSeq 2000;ILLUMINA 1 fastq
EGAD00001002749 A KNIH001 Whole-Genome Bisulfite Sequencing(WGBS) paired end data for islet cells Illumina HiSeq 2000;ILLUMINA 1 fastq
EGAD00001002171 A KNIH005 mRNA-seq paired end data for islet cells Illumina HiSeq 2000;ILLUMINA 1 fastq
EGAD00001002750 A KNIH002 Whole-Genome Bisulfite Sequencing(WGBS) paired end data for islet cells Illumina HiSeq 2000;ILLUMINA 1 fastq
EGAD00001002169 A KNIH003 mRNA-seq paired end data for islet cells Illumina HiSeq 2000;ILLUMINA 1 fastq
EGAD00001001951 HipSci - Monogenic Diabetes - Exome Sequencing - January 2016 Illumina HiSeq 2000;ILLUMINA 20 tabix,cram,vcf,bai,bam
EGAD00001002754 A KNIH006 Whole-Genome Bisulfite Sequencing(WGBS) paired end data for beta cells Illumina HiSeq 2000;ILLUMINA 1 fastq
EGAD00001002759 A KNIH011 Whole-Genome Bisulfite Sequencing(WGBS) paired end data for podocytes Illumina HiSeq 2000;ILLUMINA 1 fastq
EGAD00001002756 A KNIH008 Whole-Genome Bisulfite Sequencing(WGBS) paired end data for adipocytes Illumina HiSeq 2000;ILLUMINA 1 fastq
EGAD00001002758 A KNIH010 Whole-Genome Bisulfite Sequencing(WGBS) paired end data for podocytes Illumina HiSeq 2000;ILLUMINA 1 fastq
EGAD00001002358 RNA-Seq data for 8 erythroblast sample(s). 30 run(s), 8 experiment(s), 8 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 8 bam,fastq
EGAD00001002316 RNA-Seq data for 6 hematopoietic stem cell sample(s). 13 run(s), 6 experiment(s), 6 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 6 bam,fastq
EGAD00001002363 RNA-Seq data for 3 hematopoietic multipotent progenitor cell sample(s). 9 run(s), 3 experiment(s), 3 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 3 bam,fastq
EGAD00001002339 RNA-Seq data for 6 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 24 run(s), 6 experiment(s), 6 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 6 bam,fastq
EGAD00001002306 RNA-Seq data for 3 granulocyte monocyte progenitor cell sample(s). 3 run(s), 3 experiment(s), 3 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 3 bam,fastq
EGAD00001002433 RNA-Seq data for 4 megakaryocyte-erythroid progenitor cell sample(s). 4 run(s), 4 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 4 bam,fastq
EGAD00001002411 ChIP-Seq data for 3 T-cell Prolymphocytic Leukemia sample(s). 21 run(s), 21 experiment(s), 21 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 3 bam,fastq
EGAD00001002400 ChIP-Seq data for 9 T-cell Acute Lymphocytic Leukemia sample(s). 41 run(s), 41 experiment(s), 41 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 9 bam,fastq
EGAD00001002445 ChIP-Seq data for 3 CD3-positive, CD4-positive, CD8-positive, double positive thymocyte sample(s). 11 run(s), 11 experiment(s), 11 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 3 bam,fastq
EGAD00001002280 ChIP-Seq data for 1 Acute Lymphocytic Leukemia - CTR sample(s). 7 run(s), 7 experiment(s), 7 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,fastq
EGAD00001002406 ChIP-Seq data for 2 Acute Promyelocytic Leukemia - MC2392 sample(s). 14 run(s), 12 experiment(s), 12 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 2 bam,fastq
EGAD00001002418 ChIP-Seq data for 38 Acute Myeloid Leukemia sample(s). 244 run(s), 226 experiment(s), 226 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 38 bam,fastq
EGAD00001002384 ChIP-Seq data for 106 Chronic Lymphocytic Leukemia sample(s). 173 run(s), 162 experiment(s), 162 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 106 bam,fastq
EGAD00001002318 ChIP-Seq data for 4 neutrophilic myelocyte sample(s). 28 run(s), 23 experiment(s), 23 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 4 bam,fastq
EGAD00001002340 ChIP-Seq data for 7 Acute Myeloid Leukemia - CTR sample(s). 45 run(s), 44 experiment(s), 44 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 7 bam,fastq
EGAD00001002293 ChIP-Seq data for 2 regulatory T cell sample(s). 2 run(s), 2 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 2 bam,fastq
EGAD00001002342 ChIP-Seq data for 1 Acute Promyelocytic Leukemia - MS275 sample(s). 7 run(s), 7 experiment(s), 7 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,fastq
EGAD00001002292 ChIP-Seq data for 3 Acute Myeloid Leukemia - SAHA sample(s). 14 run(s), 14 experiment(s), 14 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 3 bam,fastq
EGAD00001002296 ChIP-Seq data for 3 monocyte - RPMI_LPS_T=24hrs_RPMI_T=5days_LPS_T=4hrs sample(s). 7 run(s), 7 experiment(s), 7 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 3 bam,fastq
EGAD00001002439 ChIP-Seq data for 3 central memory CD4-positive, alpha-beta T cell sample(s). 11 run(s), 9 experiment(s), 9 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 3 bam,fastq
EGAD00001002317 ChIP-Seq data for 7 alternatively activated macrophage sample(s). 50 run(s), 49 experiment(s), 49 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 7 bam,fastq
EGAD00001002307 ChIP-Seq data for 3 Activated B-Cell-Like Diffuse Large B-Cell Lymphoma sample(s). 12 run(s), 12 experiment(s), 12 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 3 bam,fastq
EGAD00001002420 ChIP-Seq data for 1 monocyte - T=10day_RANK_M-CSF sample(s). 2 run(s), 2 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,fastq
EGAD00001002391 ChIP-Seq data for 2 osteoclast sample(s). 17 run(s), 14 experiment(s), 14 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 2 bam,fastq
EGAD00001002362 ChIP-Seq data for 3 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 19 run(s), 18 experiment(s), 18 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 3 bam,fastq
EGAD00001002279 ChIP-Seq data for 3 monocyte - None sample(s). 17 run(s), 17 experiment(s), 17 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 3 bam,fastq
EGAD00001002372 ChIP-Seq data for 1 Acute Promyelocytic Leukemia - MC2884 (4h) sample(s). 6 run(s), 6 experiment(s), 6 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,fastq
EGAD00001002329 ChIP-Seq data for 3 Burkitt Lymphoma sample(s). 13 run(s), 13 experiment(s), 13 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 3 bam,fastq
EGAD00001002442 ChIP-Seq data for 4 germinal center B cell sample(s). 24 run(s), 22 experiment(s), 22 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 4 bam,fastq
EGAD00001002283 ChIP-Seq data for 3 effector memory CD8-positive, alpha-beta T cell sample(s). 16 run(s), 15 experiment(s), 15 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 3 bam,fastq
EGAD00001002310 ChIP-Seq data for 1 conventional dendritic cell sample(s). 4 run(s), 4 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,fastq
EGAD00001002399 ChIP-Seq data for 2 monocyte - RPMI_LPS_T=4hrs sample(s). 5 run(s), 5 experiment(s), 5 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 2 bam,fastq
EGAD00001002397 ChIP-Seq data for 5 Mantle Cell Lymphoma sample(s). 35 run(s), 35 experiment(s), 35 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 5 bam,fastq
EGAD00001002386 ChIP-Seq data for 1 CD4-positive, alpha-beta thymocyte sample(s). 3 run(s), 3 experiment(s), 3 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,fastq
EGAD00001002408 ChIP-Seq data for 3 monocyte - RPMI_BG_T=24hrs sample(s). 8 run(s), 8 experiment(s), 8 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 3 bam,fastq
EGAD00001002413 ChIP-Seq data for 3 monocyte - RPMI_T=6days sample(s). 10 run(s), 7 experiment(s), 7 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 3 bam,fastq
EGAD00001002448 ChIP-Seq data for 3 monocyte - RPMI_LPS_T=24hrs_RPMI_T=5days sample(s). 7 run(s), 7 experiment(s), 7 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 3 bam,fastq
EGAD00001002357 ChIP-Seq data for 1 Acute Promyelocytic Leukemia - MC2884 sample(s). 8 run(s), 8 experiment(s), 8 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,fastq
EGAD00001002319 ChIP-Seq data for 3 Acute Promyelocytic Leukemia - ATRA sample(s). 21 run(s), 20 experiment(s), 20 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 3 bam,fastq
EGAD00001002431 ChIP-Seq data for 1 Acute Promyelocytic Leukemia - MC3324 sample(s). 2 run(s), 1 experiment(s), 1 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,fastq
EGAD00001002344 ChIP-Seq data for 1 Acute Myeloid Leukemia - MC2884 sample(s). 3 run(s), 3 experiment(s), 3 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,fastq
EGAD00001002379 ChIP-Seq data for 4 Multiple Myeloma sample(s). 34 run(s), 28 experiment(s), 28 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 4 bam,fastq
EGAD00001002304 ChIP-Seq data for 1 Acute Promyelocytic Leukemia sample(s). 7 run(s), 7 experiment(s), 7 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,fastq
EGAD00001002421 ChIP-Seq data for 15 Acute Lymphocytic Leukemia sample(s). 79 run(s), 78 experiment(s), 78 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 15 bam,fastq
EGAD00001002281 ChIP-Seq data for 5 plasma cell sample(s). 24 run(s), 23 experiment(s), 23 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 5 bam,fastq
EGAD00001003432 ChIP-Seq data for the paper titled "Orthotopic Patient-Derived Xenografts of Pediatric Solid Tumors" Illumina HiSeq 2000;ILLUMINA 20
EGAD00001002381 ChIP-Seq data for 2 mesenchymal stem cell of the bone marrow sample(s). 16 run(s), 14 experiment(s), 14 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 2 bam,fastq
EGAD00001002282 ChIP-Seq data for 1 unswitched memory B cell sample(s). 7 run(s), 7 experiment(s), 7 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,fastq
EGAD00001002369 ChIP-Seq data for 2 CD3-negative, CD4-positive, CD8-positive, double positive thymocyte sample(s). 7 run(s), 5 experiment(s), 5 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 2 bam,fastq
EGAD00001002328 ChIP-Seq data for 3 monocyte - RPMI_T=4hrs sample(s). 8 run(s), 8 experiment(s), 8 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 3 bam,fastq
EGAD00001002444 ChIP-Seq data for 9 CD4-positive, alpha-beta T cell sample(s). 68 run(s), 63 experiment(s), 63 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 9 bam,fastq
EGAD00001002424 ChIP-Seq data for 2 endothelial cell of umbilical vein (proliferating) sample(s). 14 run(s), 14 experiment(s), 14 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 2 bam,fastq
EGAD00001002377 ChIP-Seq data for 2 erythroblast sample(s). 14 run(s), 14 experiment(s), 14 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 2 bam,fastq
EGAD00001002312 ChIP-Seq data for 1 Acute Promyelocytic Leukemia - MC2884 (24h) sample(s). 6 run(s), 6 experiment(s), 6 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,fastq
EGAD00001002389 ChIP-Seq data for 3 Lymphoma_Follicular sample(s). 11 run(s), 11 experiment(s), 11 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 3 bam,fastq
EGAD00001002435 ChIP-Seq data for 4 neutrophilic metamyelocyte sample(s). 32 run(s), 23 experiment(s), 23 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 4 bam,fastq
EGAD00001002298 ChIP-Seq data for 1 Acute Promyelocytic Leukemia - SAHA sample(s). 1 run(s), 1 experiment(s), 1 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,fastq
EGAD00001002299 RNA-Seq data for 1 CD4-positive, alpha-beta thymocyte sample(s). 1 run(s), 1 experiment(s), 1 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,fastq
EGAD00001002426 RNA-Seq data for 3 T-cell Prolymphocytic Leukemia sample(s). 3 run(s), 3 experiment(s), 3 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 3 bam,fastq
EGAD00001002365 RNA-Seq data for 1 blast forming unit erythroid sample(s). 1 run(s), 1 experiment(s), 1 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,fastq
EGAD00001002443 RNA-Seq data for 7 Acute Myeloid Leukemia - CTR sample(s). 7 run(s), 7 experiment(s), 7 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 7 bam,fastq
EGAD00001002422 RNA-Seq data for 1 CD3-negative, CD4-positive, CD8-positive, double positive thymocyte sample(s). 1 run(s), 1 experiment(s), 1 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,fastq
EGAD00001002375 RNA-Seq data for 2 monocyte sample(s). 2 run(s), 2 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 2 bam,fastq
EGAD00001002359 RNA-Seq data for 1 Acute Promyelocytic Leukemia - MC2392 sample(s). 1 run(s), 1 experiment(s), 1 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,fastq
EGAD00001002321 RNA-Seq data for 4 cytotoxic CD56-dim natural killer cell sample(s). 4 run(s), 4 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 4 bam,fastq
EGAD00001002387 RNA-Seq data for 7 alternatively activated macrophage sample(s). 9 run(s), 7 experiment(s), 7 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 7 bam,fastq
EGAD00001002345 RNA-Seq data for 2 conventional dendritic cell sample(s). 2 run(s), 2 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 2 bam,fastq
EGAD00001002446 RNA-Seq data for 3 band form neutrophil sample(s). 3 run(s), 3 experiment(s), 3 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 3 bam,fastq
EGAD00001003224 we collected tumor samples and adjacent nomal mucosae from 17 patients with colorectal cancer in surgical operation from 2014 to 2016 in the First Affiliated Hospital of Chongqing Medical University (Chongqing, China) and the Research Institute of Surgery, Third Military Medical University (Chongqing, China). the qualified captured library of each sample was then loaded on Illumina HiSeq 2000 (Illumina, San Diego, CA) platforms and subjected to high-throughput sequencing. Illumina HiSeq 2000;ILLUMINA 34
EGAD00001002343 RNA-Seq data for 2 Acute Myeloid Leukemia - SAHA sample(s). 2 run(s), 2 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 2 bam,fastq
EGAD00001002409 RNA-Seq data for 14 mature neutrophil sample(s). 14 run(s), 14 experiment(s), 13 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 13 bam,fastq
EGAD00001002315 RNA-Seq data for 6 naive B cell sample(s). 6 run(s), 6 experiment(s), 6 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 6 bam,fastq
EGAD00001002351 RNA-Seq data for 1 regulatory T cell sample(s). 1 run(s), 1 experiment(s), 1 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,fastq
EGAD00001002289 RNA-Seq data for 1 CD8-positive, alpha-beta thymocyte sample(s). 1 run(s), 1 experiment(s), 1 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,fastq
EGAD00001002326 RNA-Seq data for 2 mature eosinophil sample(s). 3 run(s), 3 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 2 bam,fastq
EGAD00001002366 RNA-Seq data for 3 neutrophilic metamyelocyte sample(s). 3 run(s), 3 experiment(s), 3 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 3 bam,fastq
EGAD00001002349 RNA-Seq data for 2 central memory CD4-positive, alpha-beta T cell sample(s). 2 run(s), 2 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 2 bam,fastq
EGAD00001002438 RNA-Seq data for 3 CD38-negative naive B cell sample(s). 3 run(s), 3 experiment(s), 3 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 3 bam,fastq
EGAD00001002402 RNA-Seq data for 1 late basophilic and polychromatophilic erythroblast sample(s). 1 run(s), 1 experiment(s), 1 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,fastq
EGAD00001002353 RNA-Seq data for 3 Acute Promyelocytic Leukemia - CTR sample(s). 3 run(s), 3 experiment(s), 3 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 3 bam,fastq
EGAD00001002320 RNA-Seq data for 1 effector memory CD8-positive, alpha-beta T cell, terminally differentiated sample(s). 1 run(s), 1 experiment(s), 1 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,fastq
EGAD00001002332 RNA-Seq data for 1 Acute Lymphocytic Leukemia - CTR sample(s). 1 run(s), 1 experiment(s), 1 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,fastq
EGAD00001002308 RNA-Seq data for 8 CD14-positive, CD16-negative classical monocyte sample(s). 8 run(s), 8 experiment(s), 8 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 8 bam,fastq
EGAD00001002417 RNA-Seq data for 6 inflammatory macrophage sample(s). 6 run(s), 6 experiment(s), 6 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 6 bam,fastq
EGAD00001002323 RNA-Seq data for 7 plasma cell sample(s). 7 run(s), 7 experiment(s), 7 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 7 bam,fastq
EGAD00001002414 RNA-Seq data for 1 unswitched memory B cell sample(s). 1 run(s), 1 experiment(s), 1 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,fastq
EGAD00001002295 RNA-Seq data for 2 CD8-positive, alpha-beta T cell sample(s). 2 run(s), 2 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 2 bam,fastq
EGAD00001002334 RNA-Seq data for 2 adult endothelial progenitor cell sample(s). 2 run(s), 2 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 2 bam,fastq
EGAD00001002347 RNA-Seq data for 1 memory B cell sample(s). 1 run(s), 1 experiment(s), 1 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,fastq
EGAD00001002429 Bisulfite-Seq data for 6 inflammatory macrophage sample(s). 83 run(s), 6 experiment(s), 12 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 6 bcf,bam
EGAD00001002364 Bisulfite-Seq data for 2 central memory CD4-positive, alpha-beta T cell sample(s). 41 run(s), 3 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 2 bcf,bam
EGAD00001002302 Bisulfite-Seq data for 1 monocyte - RPMI_LPS_T=24hrs sample(s). 22 run(s), 2 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,bcf
EGAD00001002322 Bisulfite-Seq data for 5 plasma cell sample(s). 77 run(s), 5 experiment(s), 10 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 5 bcf,bam
EGAD00001002303 Bisulfite-Seq data for 3 T-cell Prolymphocytic Leukemia sample(s). 45 run(s), 3 experiment(s), 6 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 3 bcf,bam
EGAD00001002346 Bisulfite-Seq data for 2 effector memory CD8-positive, alpha-beta T cell, terminally differentiated sample(s). 34 run(s), 3 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 2 bcf,bam
EGAD00001002440 Bisulfite-Seq data for 1 thymocyte sample(s). 14 run(s), 1 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,bcf
EGAD00001002403 Bisulfite-Seq data for 4 cytotoxic CD56-dim natural killer cell sample(s). 54 run(s), 5 experiment(s), 8 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 4 bcf,bam
EGAD00001002371 Bisulfite-Seq data for 1 monocyte - RPMI_T=6days sample(s). 14 run(s), 1 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,bcf
EGAD00001002393 Bisulfite-Seq data for 3 segmented neutrophil of bone marrow sample(s). 34 run(s), 3 experiment(s), 6 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 3 bcf,bam
EGAD00001002373 Bisulfite-Seq data for 1 macrophage - T=6days untreated sample(s). 15 run(s), 1 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,bcf
EGAD00001002327 Bisulfite-Seq data for 1 monocyte - RPMI_BG_T=1hr sample(s). 14 run(s), 1 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,bcf
EGAD00001002410 Bisulfite-Seq data for 1 macrophage - T=6days B-glucan sample(s). 15 run(s), 1 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,bcf
EGAD00001002309 Bisulfite-Seq data for 2 mature eosinophil sample(s). 23 run(s), 2 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 2 bcf,bam
EGAD00001002423 Bisulfite-Seq data for 2 erythroblast sample(s). 35 run(s), 2 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 2 bcf,bam
EGAD00001002333 Bisulfite-Seq data for 2 Acute Myeloid Leukemia - CTR sample(s). 28 run(s), 2 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 2 bcf,bam
EGAD00001002284 Bisulfite-Seq data for 3 immature conventional dendritic cell - GM-CSF_IL4_T=6_days sample(s). 61 run(s), 4 experiment(s), 6 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 3 bcf,bam
EGAD00001002407 Bisulfite-Seq data for 2 Acute Promyelocytic Leukemia - CTR sample(s). 27 run(s), 3 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 2 bcf,bam
EGAD00001002361 Bisulfite-Seq data for 3 naive B cell sample(s). 39 run(s), 3 experiment(s), 6 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 3 bcf,bam
EGAD00001002378 Bisulfite-Seq data for 3 band form neutrophil sample(s). 34 run(s), 3 experiment(s), 6 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 3 bcf,bam
EGAD00001002330 Bisulfite-Seq data for 1 precursor B cell sample(s). 6 run(s), 1 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,bcf
EGAD00001002370 Bisulfite-Seq data for 2 CD8-positive, alpha-beta thymocyte sample(s). 28 run(s), 2 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 2 bcf,bam
EGAD00001002385 Bisulfite-Seq data for 1 monocyte - RPMI_BG_T=24hrs_RPMI_T=5days sample(s). 18 run(s), 2 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,bcf
EGAD00001002396 Bisulfite-Seq data for 6 Chronic Lymphocytic Leukemia sample(s). 84 run(s), 6 experiment(s), 12 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 6 bcf,bam
EGAD00001002392 Bisulfite-Seq data for 4 Type 1 diabetes mellitus sample(s). 32 run(s), 4 experiment(s), 8 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 4 bcf,bam
EGAD00001002324 Bisulfite-Seq data for 1 monocyte - RPMI_LPS_T=24hrs_RPMI_T=5days sample(s). 15 run(s), 1 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,bcf
EGAD00001002354 Bisulfite-Seq data for 3 class switched memory B cell sample(s). 43 run(s), 4 experiment(s), 6 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 3 bcf,bam
EGAD00001002291 Bisulfite-Seq data for 1 precursor lymphocyte of B lineage sample(s). 11 run(s), 2 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,bcf
EGAD00001002434 Bisulfite-Seq data for 2 hematopoietic multipotent progenitor cell sample(s). 16 run(s), 3 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 2 bcf,bam
EGAD00001002383 Bisulfite-Seq data for 2 effector memory CD8-positive, alpha-beta T cell sample(s). 30 run(s), 3 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 2 bcf,bam
EGAD00001002428 Bisulfite-Seq data for 3 mature conventional dendritic cell - GM-CSF_IL4_T=6_days_R848_T=24hrs sample(s). 60 run(s), 4 experiment(s), 6 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 3 bcf,bam
EGAD00001002405 Bisulfite-Seq data for 1 monocyte - T=0days sample(s). 15 run(s), 1 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,bcf
EGAD00001002427 Bisulfite-Seq data for 2 osteoclast sample(s). 88 run(s), 4 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 2 bcf,bam
EGAD00001002412 Bisulfite-Seq data for 3 mature neutrophil - G-CSF/Dex. Treatment (16-20 hrs) sample(s). 33 run(s), 3 experiment(s), 6 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 3 bcf,bam
EGAD00001002335 Bisulfite-Seq data for 1 monocyte - RPMI_T=24hrs sample(s). 14 run(s), 1 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,bcf
EGAD00001002432 Bisulfite-Seq data for 1 monocyte - RPMI_LPS_T=4hrs sample(s). 18 run(s), 2 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,bcf
EGAD00001002416 Bisulfite-Seq data for 3 memory B cell sample(s). 47 run(s), 4 experiment(s), 6 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 3 bcf,bam
EGAD00001002447 Bisulfite-Seq data for 1 monocyte - RPMI_T=1hr sample(s). 15 run(s), 1 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 1 bam,bcf
EGAD00001002404 Bisulfite-Seq data for 2 adult endothelial progenitor cell sample(s). 38 run(s), 3 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 2 bcf,bam
EGAD00001002313 Bisulfite-Seq data for 7 Acute Lymphocytic Leukemia sample(s). 132 run(s), 9 experiment(s), 14 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816 Illumina HiSeq 2000;ILLUMINA 7 bcf,bam
EGAD00001002337 RNA-Seq data for 4 macrophage - T=6days LPS sample(s). 4 run(s), 4 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 4 bam,fastq
EGAD00001002360 RNA-Seq data for 4 monocyte - T=0days sample(s). 4 run(s), 4 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 4 bam,fastq
EGAD00001002338 RNA-Seq data for 4 monocyte - None sample(s). 4 run(s), 4 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 4 bam,fastq
EGAD00001002300 DNase-Hypersensitivity data for 2 monocyte - T=0days sample(s). 4 run(s), 2 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_dnaseseq_analysis_20160816 Illumina HiSeq 2000;ILLUMINA 2 bam,fastq
EGAD00001002290 DNase-Hypersensitivity data for 4 macrophage - T=6days LPS sample(s). 6 run(s), 4 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_dnaseseq_analysis_20160816 Illumina HiSeq 2000;ILLUMINA 4 bam,fastq
EGAD00001002425 DNase-Hypersensitivity data for 4 macrophage - T=6days B-glucan sample(s). 4 run(s), 4 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_dnaseseq_analysis_20160816 Illumina HiSeq 2000;ILLUMINA 4 bam,fastq
EGAD00001002398 DNase-Hypersensitivity data for 4 macrophage - T=6days untreated sample(s). 6 run(s), 4 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_dnaseseq_analysis_20160816 Illumina HiSeq 2000;ILLUMINA 4 bam,fastq
EGAD00001002663 BLUEPRINT: A human variation panel of genetic influences on epigenomes and transcriptomes in three immune cells (WGS) Illumina HiSeq 2000;ILLUMINA 197 vcf,cram
EGAD00001002697 Recurrent breast cancer is almost universally fatal. We characterize 170 patients locally relapsed or distant metastatic cancers using massively parallel sequencing. We identify that the relapse-seeding clone disseminates late from the primary tumor. TP53 and AKT1 appear to be enriched in ER-positive cancers predisposed to relapse. Mutation acquisition continues at relapse as the same mutation signatures continue to operate and new signatures, such as that caused by radiotherapy appear de novo. In 49% of cases we identify drivers mutations private to the relapse and these are sampled from a wider range of cancer genes, including SWI-SNF complex and JAK-STAT signaling. Illumina HiSeq 2000;ILLUMINA 9 bam
EGAD00001002713 DNase accessibility data for BLUEPRINT consortium immune cells included in eFORGE software tool Illumina HiSeq 2000;ILLUMINA 25 fastq,bam,readme_file
EGAD00001002712 ChIP-Seq_H3K27me3 data for 131 mature neutrophil sample(s). 321 run(s), 134 experiment(s), 134 analysis(s) on human genome GRCh37. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/blueprint_Epivar/protocols/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 131 fastq,cram,bam
EGAD00001002717 In this study we characterized genomic alterations in two to five metachronous bladder tumors from 29 patients initially diagnosed with early stage disease. Fourteen patients (32 tumors) had non progressive disease (NPD) and 15 patients (34 tumors) had progressive disease (PD). Whole exome sequencing (WES, ~50x mean read depth and whole transcriptome RNA-seq was performed (RNA was not advalible for 4 tumors). Data provided here consist of 71 unmapped Bam files form whole transcriptome RNA-seq. Illumina HiSeq 2000;ILLUMINA 71 bam
EGAD00001002718 In this study we characterized genomic alterations in two to five metachronous bladder tumors from 29 patients initially diagnosed with early stage disease. Fourteen patients (32 tumors) had non progressive disease (NPD) and 15 patients (34 tumors) had progressive disease (PD). Whole exome sequencing (WES, ~50x mean read depth and whole transcriptome RNA-seq was performed (RNA was not advalible for 4 tumors). Data provided here consist of 71 mapped Bam files form whole transcriptome RNA-seq. Illumina HiSeq 2000;ILLUMINA 71 bam
EGAD00001002667 Additional files for "The Genomic Landscape of Core-Binding Factor Acute Myeloid Leukemias" (EGAS00001000349). This dataset includes the processed Excap data referenced in this paper. Illumina HiSeq 2000;ILLUMINA 327 bam
EGAD00001002711 ChIP-Seq_H3K4me3 data for 133 mature neutrophil sample(s). 208 run(s), 136 experiment(s), 136 analysis(s) on human genome GRCh37. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/blueprint_Epivar/protocols/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;ILLUMINA 133 fastq,cram,bam
EGAD00001002530 Additional files for "The Genomic Landscape of Core-Binding Factor Acute Myeloid Leukemias" (EGAS00001000349). This dataset includes the processed RNASeq data referenced in this paper. Illumina HiSeq 2000;ILLUMINA 36 bam
EGAD00001002676 DATA FILES FOR PCGP SJERG (WGS) Illumina HiSeq 2000;ILLUMINA 44 bam
EGAD00001002677 DATA FILES FOR PCGP SJERG (WXS) Illumina HiSeq 2000;ILLUMINA 42 bam
EGAD00001002680 This dataset contains RNA-Seq files for the SJACT cohort associated with the paper "Genetic landscape of pediatric Adrenocortical Tumor". In this paper, we analyse 37 adrenocortical tumours (ACTs) by whole-genome, whole-exome and/or transcriptome sequencing. Illumina HiSeq 2000;ILLUMINA 26 bam
EGAD00001001950 HipSci - Bardet-Biedl Syndrome - Exome Sequencing - January 2016 Illumina HiSeq 2000;ILLUMINA 20 tabix,cram,vcf,bai,bam
EGAD00001002692 DATA FILES FOR MULLIGHAN MEF2D RNASEQ STRANDED Illumina HiSeq 2000;ILLUMINA 200 bam
EGAD00001002170 A KNIH004 mRNA-seq paired end data for islet cells Illumina HiSeq 2000;ILLUMINA 1 fastq
EGAD00001002751 A KNIH003 Whole-Genome Bisulfite Sequencing(WGBS) paired end data for islet cells Illumina HiSeq 2000;ILLUMINA 1 fastq
EGAD00001002752 A KNIH004 Whole-Genome Bisulfite Sequencing(WGBS) paired end data for islet cells Illumina HiSeq 2000;ILLUMINA 1 fastq
EGAD00001002753 A KNIH005 Whole-Genome Bisulfite Sequencing(WGBS) paired end data for islet cells Illumina HiSeq 2000;ILLUMINA 1 fastq
EGAD00001001954 HipSci - Bardet-Biedl Syndrome - RNA Sequencing - January 2016 Illumina HiSeq 2000;ILLUMINA 19 other,cram,bai,bam
EGAD00001001952 HipSci - Bardet-Biedl Syndrome - RNA Sequencing - April 2015 Illumina HiSeq 2000;ILLUMINA 3 other,cram,bai,bam
EGAD00001002721 Whole genome sequencing of 300 individuals from 142 diverse populations Illumina HiSeq 2000;ILLUMINA 21 bam
EGAD00001003390 DCM-cases (149 human DCM samples) human heart biopsies from 149 patients with dilated cardiomyopathy (DCM) were subjected to RNA sequencing in order to assess transcriptome variation. We used Illumina HiSeq2000 technology. Each sample-dataset contains the output from tophat-1.4.1 (one *.bam file with the aligned reads and two *.fq files one with the not aligned forward read and one with the revers unaligned reads). We reveal extensive differences of gene expression and splicing between dilated cardiomyopathy patients and controls. Illumina HiSeq 2000;ILLUMINA 149
EGAD00001002725 Autism spectrum disorder (ASD) is a collection of neuro-developmental disorders characterized by deficits in social interaction and social communication, along with restricted and repetitive behaviour patterns. we globally interrogated the histone acetylomes of enhancers in a large cohort of ASD and control samples by analyzing tissue from three brain regions postmortem: prefrontal cortex (PFC), temporal cortex (TC) and cerebellum (CB). H3K27ac was selected as the representative acetylation mark and 288 ChIP-seq were performed on these postmortem samples. Illumina HiSeq 2000;ILLUMINA 291 bam
EGAD00001002714 We recruited 100 healthy, male donors of self-reported European descent (EUB) and 100 of self-reported African descent (AFB) (Ghent, Belgium). For each participant, peripheral blood mononuclear cells (PBMCs) were isolated from whole blood on Ficoll-Paque density gradients. Monocytes were then positively selected with magnetic CD14 microbeads and exposed for 6 hours to different ligands activating TLR4 (LPS), TLR1/2 (Pam3CSK4), TLR7/8 (R848) and to a human seasonal influenza A virus (IAV). High-quality RNA was obtained from unstimulated and stimulated monocytes for 970 of the 1000 samples (200 x 5 conditions), and was sequenced on an Illumina HiSeq2000. On average, 34 million 101-bp single-end reads were obtained per sample. Illumina HiSeq 2000;ILLUMINA 970 fastq
EGAD00001002715 Exome sequencing of isolate populations and Generation Scotland Illumina HiSeq 2000;ILLUMINA 1,027 bam
EGAD00001002741 Additional Xenograph files for PCGP SJERG Illumina HiSeq 2000;ILLUMINA 11 bam
EGAD00001002707 Whole exome sequencing of a normal sample, primary tumor sample, and relapse tumor sample of a transformed non-Hodgkins follicular lymphoma patient with extraordinary response to treatment. Illumina HiSeq 2000;ILLUMINA 3 fastq
EGAD00001002704 DATA FILES FOR MULLIGHAN MEF2D RNASEQ UNSTRANDED Illumina HiSeq 2000;ILLUMINA 217 bam
EGAD00001002746 Illumina HiSeq 2000;ILLUMINA 13 bam
EGAD00001002773 As part of the International Parkinson Disease Genomics Consortium, exomes of Parkinson disease (PD) patients and healthy controls were sequenced to study the genetic etiology of PD. The Dutch cohort consists of 175 patients with a young age of onset below 50 years. Researchers can apply for access to fastq files for this cohort. Illumina HiSeq 2000;ILLUMINA 211 fastq
EGAD00001002657 Reverse Capture Hi-C Illumina HiSeq 2000;ILLUMINA 8 fastq
EGAD00001002268 PCHiC Illumina HiSeq 2000;ILLUMINA 53 fastq
EGAD00001002969 Bisulfite-Seq data for 1 sample(s) Acute Lymphocytic Leukemia for precursor B cell from bone marrow, on Genome GRCh38. 3 run(s), 1 experiment(s), 0 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000;ILLUMINA 1 bam
EGAD00001002932 ChIPmentation data for 1 sample(s) for germinal center B cell from tonsil, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016). Illumina HiSeq 2000;ILLUMINA 1 bam,fastq
EGAD00001002948 ChIP-Seq data for 1 sample(s) for conventional dendritic cell from cord blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000;ILLUMINA 1 bam,fastq
EGAD00001002951 ChIP-Seq data for 1 sample(s) for class switched memory B cell from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000;ILLUMINA 1 bam,fastq
EGAD00001002885 Raw sequence data, fastq format Illumina HiSeq 2000;ILLUMINA 26 fastq
EGAD00001002950 ChIP-Seq data for 1 sample(s) for memory B cell from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000;ILLUMINA 1 bam,fastq
EGAD00001002937 ChIPmentation data for 1 sample(s) for naive B cell from tonsil, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016). Illumina HiSeq 2000;ILLUMINA 1 bam,fastq
EGAD00001002949 ChIP-Seq data for 1 sample(s) Acute Lymphocytic Leukemia for precursor B cell from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000;ILLUMINA 1 bam,fastq
EGAD00001002952 ChIP-Seq data for 4 sample(s) T-cell Acute Lymphocytic Leukemia from capillary blood, on Genome GRCh38. 7 run(s), 7 experiment(s), 7 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000;ILLUMINA 4 bam,fastq
EGAD00001002962 RNA-Seq data for 1 sample(s) Acute Myeloid Leukemia for blast cell from bone marrow, on Genome GRCh38. 1 run(s), 1 experiment(s), 0 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000;ILLUMINA 1 fastq
EGAD00001002961 RNA-Seq data for 1 sample(s) for monocyte T=10day_S100A9_RANKL_M-CSF from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 0 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000;ILLUMINA 1 fastq
EGAD00001002959 RNA-Seq data for 1 sample(s) for monocyte T=1day_M-CSF_S100A9_4hr_RANL from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 0 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000;ILLUMINA 1 fastq
EGAD00001002960 RNA-Seq data for 1 sample(s) for monocyte T=6day_S100A9_RANKL_M-CSF from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 0 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000;ILLUMINA 1 fastq
EGAD00001002967 RNA-Seq data for 1 sample(s) for monocyte T=6day_RANK_M-CSF from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 0 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000;ILLUMINA 1 fastq
EGAD00001002965 RNA-Seq data for 1 sample(s) for monocyte T=2day_S100A9_RANKL_M-CSF from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 0 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000;ILLUMINA 1 fastq
EGAD00001002968 RNA-Seq data for 2 sample(s) Acute Myeloid Leukemia for myeloid cell from venous blood, on Genome GRCh38. 2 run(s), 2 experiment(s), 0 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000;ILLUMINA 2 fastq
EGAD00001002956 RNA-Seq data for 2 sample(s) T-cell lymphoma for helper T cell from venous blood, on Genome GRCh38. 2 run(s), 2 experiment(s), 0 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000;ILLUMINA 2 fastq
EGAD00001002957 RNA-Seq data for 1 sample(s) for monocyte T=2day_RANK_M-CSF from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 0 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000;ILLUMINA 1 fastq
EGAD00001002963 RNA-Seq data for 6 sample(s) Acute Lymphocytic Leukemia for precursor B cell from venous blood, on Genome GRCh38. 6 run(s), 6 experiment(s), 0 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000;ILLUMINA 6 fastq
EGAD00001002964 RNA-Seq data for 1 sample(s) for monocyte T=1day_4hr_RANK from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 0 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000;ILLUMINA 1 fastq
EGAD00001002954 RNA-Seq data for 1 sample(s) Acute Lymphocytic Leukemia from bone marrow, on Genome GRCh38. 1 run(s), 1 experiment(s), 0 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000;ILLUMINA 1 fastq
EGAD00001002953 RNA-Seq data for 8 sample(s) Acute Lymphocytic Leukemia for precursor B cell from bone marrow, on Genome GRCh38. 8 run(s), 8 experiment(s), 0 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000;ILLUMINA 8 fastq
EGAD00001002966 RNA-Seq data for 1 sample(s) for monocyte T=10day_RANK_M-CSF from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 0 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000;ILLUMINA 1 fastq
EGAD00001002955 RNA-Seq data for 1 sample(s) for monocyte T=0day from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 0 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000;ILLUMINA 1 fastq
EGAD00001002958 RNA-Seq data for 1 sample(s) Acute Myeloid Leukemia from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 0 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000;ILLUMINA 1 fastq
EGAD00001002947 ChIP-Seq data for 5 sample(s) for thymocyte from thymus, on Genome GRCh38. 17 run(s), 17 experiment(s), 17 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000;ILLUMINA 5 bam,fastq
EGAD00001002886 Exome sequencing of North American Brain Expression Consortium (NABEC) subject. Illumina HiSeq 2000;ILLUMINA 298 fastq
EGAD00001003348 The differentiation of distinct multifocal hepatocellular carcinoma (HCC): multicentric disease vs. intrahepatic metastases, in which the management and prognosis varies substantively, remains problematic. We aim to stratify multifocal HCC and identify novel diagnostic and prognostic biomarkers by performing whole genome and transcriptome sequencing, as part of a multi-omics strategy. Illumina HiSeq 2000;ILLUMINA 8
EGAD00001003347 This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ This dataset contains all the data available for this study on 2017-05-24. Illumina HiSeq 2000;ILLUMINA 76
EGAD00001002152 Whole exome sequencing for the matched germline and tumor DNA from 10 ALL cases with ZNF384 rearrangements. Illumina HiSeq 2000;ILLUMINA 20 fastq
EGAD00001002151 Whole transcriptome sequencing of 231 children with newly-diagnosed ALL Illumina HiSeq 2000;ILLUMINA 231 fastq
EGAD00001002716 In this study we characterized genomic alterations in two to five metachronous bladder tumors from 29 patients initially diagnosed with early stage disease. Fourteen patients (32 tumors) had non progressive disease (NPD) and 15 patients (34 tumors) had progressive disease (PD). Whole exome sequencing (WES, ~50x mean read depth and whole transcriptome RNA-seq was performed (RNA was not advalible for 4 tumors) Data provided here consist of 122 Bam files for WES (83 Tumors and 39 blood) Illumina HiSeq 2000;ILLUMINA 122 bam
EGAD00001003096 As part of the International Parkinson's Disease Genomics Consortium, exomes of Parkinson's disease (PD) patients and healthy controls were sequenced to study the genetic etiology of PD. This UK cohort consists of 70 PD patients. Researchers can apply for access to fastq files for this cohort. Illumina HiSeq 2000;ILLUMINA 77 fastq
EGAD00001002896 Amplicon sequencing libraries from the study "Histological Transformation and Progression in Follicular Lymphoma: a Clonal Evolution Study". These are Illumina amplicon deep sequencing libraries (n = 118) to validate somatic predictions made in the whole genome sequencing libraries. Specifically, there are 72 tumor libraries and 46 normal libraries. Some patients may have multiple amplicon libraries sequenced. Illumina HiSeq 2000;ILLUMINA 118
EGAD00001003100 UKBEC 1st release of Exome data for 65 neuropathologically confirmed control individuals of European descent. Illumina HiSeq 2000;ILLUMINA 65
EGAD00001002730 SPEED - childhood dystonia KMT2B dataset Illumina HiSeq 2000;ILLUMINA 5
EGAD00001003106 Human HiC Illumina HiSeq 2000;ILLUMINA 16
EGAD00001002738 Background: In follicular lymphoma (FL), studies addressing the prognostic value of microenvironment-related immunohistochemical (IHC) markers and tumor cell-related genetic markers have yielded conflicting results, precluding implementation in practice. Therefore, the Lunenburg Lymphoma Biomarker Consortium (LLBC) performed a validation study for published markers. Methods: To maximize sensitivity, an end-of-spectrum design was applied for 122 uniformly immunochemotherapy-treated FL patients retrieved from international trials and registries; early failure (EF): progression or lymphoma-related death <2 years versus long remission: response duration of >5 years. IHC staining for T-cells and macrophages was performed on tissue microarrays from initial biopsy and scored with a validated computer-assisted protocol. Shallow whole-genome and deep targeted sequencing was performed on the same samples. Results: 96/122 cases with complete molecular and immunohistochemical data were included in the analysis. EZH2 wild-type (p=0.006), gain of chromosome 18 (p=0.002), low percentages of CD8+ cells (p=0.011) and CD163+ areas (p=0.038) were associated with EF. No significant differences in other markers were observed, thereby refuting previous claims on their prognostic significance. Conclusion: Using an optimized study design, this LLBC study validates wild-type EZH2 status, gain of chromosome 18, low percentages of CD8+ cells and CD163+ area as predictors of EF to immunochemotherapy in FL. Illumina HiSeq 2000;ILLUMINA 96
EGAD00001002731 whole exome sequencing of tumor- as well as PBMC-derived DNA of five melanoma patients for identification of naturally presented patient-specific neoepitopes Illumina HiSeq 2000;ILLUMINA 10
EGAD00001002883 RNAseq on Illumina HiSeq2000/2500 of Patient-derived xenograft derived from colorectal cancer sample of a validation cohort of 60 PDX Illumina HiSeq 2000;ILLUMINA 60
EGAD00001002884 RNAseq on Illumina HiSeq2000/2500 of PDO culture derived from colorectal cancer metastasis sample at early/late passages Illumina HiSeq 2000;ILLUMINA 8
EGAD00001003160 Exome data from patients and parents with DONSON mutations Illumina HiSeq 2000;ILLUMINA 15
EGAD00001003135 DATA FILES FOR GRUBER SJAMLM7 RNASEQ Illumina HiSeq 2000;ILLUMINA 86
EGAD00001003134 DATA FILES FOR GRUBER SJAMLM7 EXOME Illumina HiSeq 2000;ILLUMINA 114
EGAD00001003133 RRBS data of 86 Ewing patients (French). Illumina HiSeq 2000/2500 (Fastq files available). Sheffield et al. Nat Med. 2017 Jan 30 Illumina HiSeq 2000;ILLUMINA 86
EGAD00001002893 This dataset contains all RNA-seq runs for the BLN panel of cell lines and matched parental tumors. Tumor/cell line pairs have been authenticated using SNP profiles and all pairs were confirmed. Please note: The dataset also contains raw data from an early primary culture (BLN-1) where no stable cell line could be generated. Please also note different reference genomes. Illumina HiSeq 2000;ILLUMINA 21
EGAD00001003163 Whole genome sequencing data of 20 carcinosarcomas. Illumina HiSeq 2000;ILLUMINA 23
EGAD00001003115 Whole genome sequencing data of 15 French Caucasian and 10 African-Caribbean men with prostate Cancer. Illumina HiSeq 2000;ILLUMINA 50
EGAD00001003092 Using sequencing and gene expression analyses, we identified a subgroup of HCA characterized by fusion of the INHBE and GLI1 genes and activation of sonic hedgehog pathway. Molecular subtypes of HCAs associated with different patients’ risk factors for HCA, disease progression, and pathology features of tumors. This classification system might be used to select treatment strategies for patients with HCA. Related Publication: Molecular Classification of Hepatocellular Adenoma Associates With Risk Factors, Bleeding, and Malignant Transformation Nault, Jean-CharlesLaurent, Christophe et al. Gastroenterology , Volume 152 , Issue 4 , 880 - 894.e6 http://dx.doi.org/10.1053/j.gastro.2016.11.042 Illumina HiSeq 2000;ILLUMINA 21
EGAD00001001955 HipSci - Monogenic Diabetes - RNA Sequencing - January 2016 Illumina HiSeq 2000;ILLUMINA 20
EGAD00001003174 There are 116 liver cancer cases in this study and belong to LICA-CN project Illumina HiSeq 2000;ILLUMINA 232
EGAD00001003237 Primary mucosal melanomas (MMs) arise from melanocytes located in mucosal membranes lining the respiratory, gastrointestinal and urogenital tracts. MMs frequently present late and have a poor prognosis; the 5-year survival rate is only 14%. MM makes up only ~1.4% of all melanomas and it is this rarity that makes knowledge of the genetic changes that contribute to its pathogenesis limited to a small number of exome/genome studies and other targeted studies. Thus to investigate the somatic alterations and mutation spectra in MM genomes, we have extracted genomic DNA from formalin-fixed, paraffin-embedded (FFPE) human MMs, and subjected them to whole exome sequencing. Given the propensity of MM to metastasize, we will also be sequencing metastatic MM lesions; primary and metastatic lesions from the same individual represent an excellent opportunity to identify potential drivers of metastasis in MM. Finally we will sequence 'normal' DNA from the same individual, where possible, to exclude germline variations. Illumina HiSeq 2000;ILLUMINA 141
EGAD00001003239 This study involves mutagenizing C32, a melanoma cell line, with ENU to identify those mutations which engender resistance to a targeted treatment. Illumina HiSeq 2000;ILLUMINA 80
EGAD00001003241 Toxoplasmosis is a zoonotic disease caused by a ubiquitous protozoan parasite called Toxoplasma gondii, which can infect all mammal and bird species throughout the world. seroprevalence varies widely between countries. Studies have estimated that between 7-34% of people in the UK have been infected with T. gondii. The vast majority of these people will not have noticed any symptoms, however about 10% of people develop a mild to moderate self limiting flu-like illness. Following the acute active stage of the infection the parasite persists in the body in the form of cysts, particularly in heart and skeletal muscle and nervous system tissues, for many years, and usually for life. In immunocompetent persons these cysts do not pose a health risk. We will use RNA-seq to quantify the transcriptional response of macrophages to T gondii infection. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina HiSeq 2000;ILLUMINA 18
EGAD00001003244 We aim to sequence the mRNA transcriptome of 22 human melanoma cell lines in biological triplicate in order to define the gene expression profile of each cell line. The data will be correlated to the mutation status and the sensitivity to a panel of drugs in order to identify genes whose deregulation is associated to drug resistance This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina HiSeq 2000;ILLUMINA 66
EGAD00001003242 This study comprises of three different datasets. 1) 57 samples from the 1243 canapps cell line study,2) 91 FFPE normal samples and 3) 87 samples from the SCORT WS2 dataset. The aim is to sequence these 235 samples in order to test the new V2 Colorectal bait design. Illumina HiSeq 2000;ILLUMINA 92
EGAD00001003250 1cm biospies of from patients undergoing bladder cystectomy will be collected. The underlying muscle and stroma will be removed and the remaining epithelia dissected into small sequential areas which will be sent for ultra-deep exome sequencing using a panel of known cancer and viral genes. Sequence analysis using similar methods to Martincorena I et al (Science 2015, 348:880) will provide an idea of the somatic mutational landscape in these patient samples. Individual patient muscle samples will also be sequenced as a reference. Illumina HiSeq 2000;ILLUMINA 55
EGAD00001003252 Sequencing of drug resistant organoids Illumina HiSeq 2000;ILLUMINA 36
EGAD00001003253 Targeted gene screen of cell line tumour samples for testing the new V2 Colorectal gene panel. Illumina HiSeq 2000;ILLUMINA 57
EGAD00001003189 Whole genome sequencing of 8 HER2-Positive Breast Cancer (in complement to EGAD00001001844) Illumina HiSeq 2000;ILLUMINA 16
EGAD00001003259 Regions of common inter-individual DNA methylation differences in human monocytes – potential function and genetic basis WGBS Data of Samples: 43_Hm03_BlMo_Ct, 43_Hm02_BlMo_Ct, 43_Hm05_BlMo_Ct, 43_Hm01_BlMo_Ct For details about sequencing or sample metadata check http://deep.dkfz.de/ Illumina HiSeq 2000;ILLUMINA 4
EGAD00001003225 ICGC prostate UK study batches 4-6 prostatectomy analysis. Whole genome sequenced normal (blood) and malignant tissue pair of 111 patients. Illumina HiSeq 2000;ILLUMINA 221
EGAD00001002686 CD4 T-Cell ChIP-Seq Illumina HiSeq 2000;ILLUMINA 42
EGAD00001002687 CD4 T-Cell RNA-Seq Illumina HiSeq 2000;ILLUMINA 4
EGAD00001003281 Genomic alterations driving tumorigenesis result from the interaction of environmental exposures and endogeneous cellular processes. With a diversity of risk factors including viral infection, carcinogenic exposures and metabolic diseases, liver cancer is an ideal model to study these interactions. Whole genome sequencing of liver tumors identified 10 mutational signatures showing distinct relationships with environmental exposures, replication and transcription. Transcription-coupled damage was specifically associated with the liver-specific signature 16 and alcohol intake. Flood of indels were identified in very highly expressed hepato-specific genes, likely resulting from replication-transcription collisions. Reconstruction of sub-clonal architecture revealed mutational signature evolution during tumor development exemplified by the vanishing of aflatoxin-B1 signature in African migrants. These findings shed new light on the natural history of liver cancers. Illumina HiSeq 2000;ILLUMINA 52
EGAD00001003292 Illumina HiSeq 2000;ILLUMINA 520
EGAD00001003218 There are 80 Brain cancer cases (160 samples)in this study and belong to GBM-CN project. Illumina HiSeq 2000;ILLUMINA 80
EGAD00001003266 For ENOC cohorts, OvCaRe cases were reviewed, including frozen material, by at least two expert gynecopathologists prior to inclusion in the sequencing cohort who provided the confirmation on final selected cohort. Frozen H&E from Tokyo were also used for evaluation along with representative H&E photos and review done at the Jikei School of Medicine. For ENOC, DAH985 and DG1288 are recurrent and both were treated with chemotherapy after their first surgery. DAH123 is a untreated sample, metastasis from an primary endometrial tumour. All HGSC, GCT, CCOC and the rest ENOC tumours are primary tumour samples. Library construction and sequencing Frozen specimens with >50% tumour cellularity (based on initial slide review) were used for cryosectioning and subsequent nucleic acid extraction. Patient tumour and normal blood samples derived from primary, untreated fresh frozen tumour specimens harvested at diagnosis during standard of care debulking surgery. Germline DNA was provided from peripheral blood buffy coat on all specimens except 13 from Tokyo, where non-cancer frozen tissue was used as a germline source. DNA extraction from both matched normal (blood) and tumour samples (frozen tissue) were performed using the QIAamp Blood and Tissue DNA kit (Qiagen) and quantified using a Qbit fluorometer and reagents (high-sensitivity assay). Three lanes of Illumina HiSeq 2500 v4 chemistry for normal samples and five lanes for tumour samples were obtained. The PCR-free protocol was adopted to eliminate the PCR-induced bias and improve coverage across the genome. Illumina HiSeq 2000;ILLUMINA 58
EGAD00001003267 For GCT cohorts, OvCaRe cases were reviewed, including frozen material, by at least two expert gynecopathologists prior to inclusion in the sequencing cohort who provided the confirmation on final selected cohort. Frozen H&E from Tokyo were also used for evaluation along with representative H&E photos and review done at the Jikei School of Medicine. All GCT tumours are primary tumour samples. Library construction and sequencing Frozen specimens with >50% tumour cellularity (based on initial slide review) were used for cryosectioning and subsequent nucleic acid extraction. Patient tumour and normal blood samples derived from primary, untreated fresh frozen tumour specimens harvested at diagnosis during standard of care debulking surgery. Germline DNA was provided from peripheral blood buffy coat on all specimens except 13 from Tokyo, where non-cancer frozen tissue was used as a germline source. DNA extraction from both matched normal (blood) and tumour samples (frozen tissue) were performed using the QIAamp Blood and Tissue DNA kit (Qiagen) and quantified using a Qbit fluorometer and reagents (high-sensitivity assay). Three lanes of Illumina HiSeq 2500 v4 chemistry for normal samples and five lanes for tumour samples were obtained. The PCR-free protocol was adopted to eliminate the PCR-induced bias and improve coverage across the genome. Illumina HiSeq 2000;ILLUMINA 20
EGAD00001003308 This is an in vitro genome-wide CRISPR/cas9 screen in human glioblastoma stem cells, screening for genes essential for survival of these cells. These cells express cas9 and have been transfected with a guide RNA library causing gene knockouts. We will analyse the sequencing data for depletion of guide RNAs. This dataset contains all the data available for this study on 2017-04-27. Illumina HiSeq 2000;ILLUMINA 10
EGAD00001003268 HGSC cases in the OvCaRe and CRCHUM Tumour Banks were selected according to the following criteria: (i) were administered platinum taxane based therapy; (ii) relapsed within 12 months (365 days) or had at least longer than 4.5 years (1642.5 days) follow-up data; (iii) had at least 50% tumour content by H&E staining and expert pathology review. All cases were re-reviewed by expert pathologists to confirm the diagnosis of HGSC. Germline BRCA1 and BRCA2 was determined for all patients through hereditary cancer screening programs. The design of cases selection as a discovery cohort was engineered to amplify biological differences by selecting cases from the extremes of the outcome distribution. All HGSC tumours are primary tumour samples. Library construction and sequencing Frozen specimens with >50% tumour cellularity (based on initial slide review) were used for cryosectioning and subsequent nucleic acid extraction. Patient tumour and normal blood samples derived from primary, untreated fresh frozen tumour specimens harvested at diagnosis during standard of care debulking surgery. Germline DNA was provided from peripheral blood buffy coat on all specimens except 13 from Tokyo, where non-cancer frozen tissue was used as a germline source. DNA extraction from both matched normal (blood) and tumour samples (frozen tissue) were performed using the QIAamp Blood and Tissue DNA kit (Qiagen) and quantified using a Qbit fluorometer and reagents (high-sensitivity assay). Three lanes of Illumina HiSeq 2500 v4 chemistry for normal samples and five lanes for tumour samples were obtained. The PCR-free protocol was adopted to eliminate the PCR-induced bias and improve coverage across the genome. Illumina HiSeq 2000;ILLUMINA 118
EGAD00001003321 Systematic next generation sequencing efforts are beginning to define the genomic landscape across a range of primary tumours, but we know very little of the mutational evolution that contributes to disease progression. We therefore propose to obtain a comprehensive description of genomic, transcriptomic and epigenomic changes in a cohort of matched primary and metastatic colorectal cancers, and additionally to explore the extent to which those mutations identified as recurrent in the metastatic setting are able to subvert normal biological processes using both genetically engineered mouse models and established cancer cell lines. This study will enable us to define to what extent primary tumour profiling can capture the biological processes operative in matched metastases as well as the significance of intratumoural heterogeneity. This dataset contains all the data available for this study on 2017-05-04. Illumina HiSeq 2000;ILLUMINA 523
EGAD00001003330 The samples will be sequenced for a targeted panel of cancer relevant genes (n ~ 370) and analysed for somatic mutations. This dataset contains all the data available for this study on 2017-05-11. Illumina HiSeq 2000;ILLUMINA 416
EGAD00001003334 Targeted exome sequencing of patient derived xenografts from primary colorectal tumours and liver metastases. This dataset contains all the data available for this study on 2017-05-11. Illumina HiSeq 2000;ILLUMINA 573
EGAD00001003339 Whole exome library making will be performed on genomic DNA derived from radiotherapy induced sarcoma samples and matched normal DNA from the same patients. Next Generation sequencing will be performed on the resulting libraries and mapped to build 37 of the human reference genome to facilitate the identification of mutations This dataset contains all the data available for this study on 2017-05-17. Illumina HiSeq 2000;ILLUMINA 7
EGAD00001003231 Poly A transcriptome sequence of mutifocal hepatocelular carcinoma Illumina HiSeq 2000;ILLUMINA 7
EGAD00001003306 Exome sequencing data of 15 French Caucasian and 10 African-Caribbean men with prostate Cancer. Illumina HiSeq 2000;ILLUMINA 50
EGAD00001002654 This dataset contains RNA-seq, ATAC-seq, and ChIP-seq samples from the SJERG cohort. We applied ChIP-Seq for Dux4 on two B-cell ALL cell-lines(REH, Nalm6) along with INPUT. ATAC-Seq on two B-cell ALL cell-lines(REH, Nalm6) and xenograft of a B-cell ALL patient(ERG000016). Illumina HiSeq 2000;ILLUMINA 13
EGAD00001001422 HipSci - Bardet-Biedl Syndrome - Exome Sequencing - April 2015 Illumina HiSeq 2000;ILLUMINA 3
EGAD00001003392 High-coverage WGS sequencing of DNA samples from 51pairs GCs was performed on the Illumina HiSeq X Ten System. Illumina HiSeq 2000;ILLUMINA 102
EGAD00001003279 RNA sequencing data for 170 medulloblastoma tumor samples Illumina HiSeq 2000;ILLUMINA 171
EGAD00001003391 DCM-controls (113 human non-DCM samples) human heart biopsies from 113 non-diseased controls were subjected to RNA sequencing in order to assess transcriptome variation. We used Illumina HiSeq2000 technology. Each sample-dataset contains the output from tophat-1.4.1 (one *.bam file with the aligned reads and two *.fq files one with the not aligned forward read and one with the revers unaligned reads). We reveal extensive differences of gene expression and splicing between dilated cardiomyopathy patients and controls. Illumina HiSeq 2000;ILLUMINA 113
EGAD00001003405 High-coverage WGS sequencing of DNA samples from 23pairs GCs was performed on the Illumina HiSeq X Ten System. Illumina HiSeq 2000;ILLUMINA 46
EGAD00001003230 Small RNA expression profiles of the blood plasma-derived exosomes from B-cell chronic lymphocytic leukemia patients Illumina HiSeq 2000;ILLUMINA 3
EGAD00001003311 Dataset contains one sample derived from gDNA of human fibroblasts. Files are in FASTQ format and were generated using the Agilent SureSelect Human All Exon 50Mb Kit and followed by Next Generation Sequencing on a HighSeq2000 instrument (Illumina). Illumina HiSeq 2000;ILLUMINA 1
EGAD00001003367 RNAseq on Illumina HiSeq2000/2500 of colorectal cancer primary tumor sample (OT2_cohort) Illumina HiSeq 2000;ILLUMINA 7
EGAD00001003376 Whole-genome sequencing on Illumina HiSeq2000/2500 of Patient-derived xenograft derived from colorectal cancer primary tumor sample (OT2_cohort) Illumina HiSeq 2000;ILLUMINA 12
EGAD00001003371 Whole-genome sequencing on Illumina HiSeq2000/2500 of normal colon control tissue (OT2_cohort) Illumina HiSeq 2000;ILLUMINA 1
EGAD00001003364 RNAseq on Illumina HiSeq2000/2500 of colorectal cancer metastasis sample (OT2_cohort) Illumina HiSeq 2000;ILLUMINA 4
EGAD00001003375 Whole-genome sequencing on Illumina HiSeq2000/2500 of colorectal cancer primary tumor sample (OT2_cohort) Illumina HiSeq 2000;ILLUMINA 7
EGAD00001003365 RNAseq on Illumina HiSeq2000/2500 of PDO culture derived from colorectal cancer metastasis sample (OT2_cohort) Illumina HiSeq 2000;ILLUMINA 1
EGAD00001003378 Whole-exome sequencing on Illumina HiSeq2000/2500 of normal colon control tissue (OT2_cohort) Illumina HiSeq 2000;ILLUMINA 1
EGAD00001003377 Whole-exome sequencing on Illumina HiSeq2000/2500 of Blood EDTA (OT2_cohort) Illumina HiSeq 2000;ILLUMINA 10
EGAD00001003379 Whole-exome sequencing on Illumina HiSeq2000/2500 of colorectal cancer metastasis sample (OT2_cohort) Illumina HiSeq 2000;ILLUMINA 4
EGAD00001003383 Whole-exome sequencing on Illumina HiSeq2000/2500 of colorectal cancer primary tumor sample (OT2_cohort) Illumina HiSeq 2000;ILLUMINA 7
EGAD00001003363 Whole-exome sequencing on Illumina HiSeq2000/2500 of Patient-derived xenograft derived from colorectal cancer primary tumor sample (EPO2_cohort) Illumina HiSeq 2000;ILLUMINA 114
EGAD00001003362 RNAseq on Illumina HiSeq2000/2500 of Patient-derived xenograft derived from colorectal cancer primary tumor sample (EPO2_cohort) Illumina HiSeq 2000;ILLUMINA 49
EGAD00001003369 RNAseq on Illumina HiSeq2000/2500 of Patient-derived xenograft derived from colorectal cancer primary tumor sample (OT2_cohort) Illumina HiSeq 2000;ILLUMINA 13
EGAD00001003374 Whole-genome sequencing on Illumina HiSeq2000/2500 of Patient-derived xenograft derived from colorectal cancer metastasis sample (OT2_cohort) Illumina HiSeq 2000;ILLUMINA 8
EGAD00001003366 RNAseq on Illumina HiSeq2000/2500 of Patient-derived xenograft derived from colorectal cancer metastasis sample (OT2_cohort) Illumina HiSeq 2000;ILLUMINA 10
EGAD00001003373 Whole-genome sequencing on Illumina HiSeq2000/2500 of PDO culture derived from colorectal cancer metastasis sample (OT2_cohort) Illumina HiSeq 2000;ILLUMINA 1
EGAD00001003381 Whole-exome sequencing on Illumina HiSeq2000/2500 of Patient-derived xenograft derived from colorectal cancer metastasis sample (OT2_cohort) Illumina HiSeq 2000;ILLUMINA 10
EGAD00001003372 Whole-genome sequencing on Illumina HiSeq2000/2500 of colorectal cancer metastasis sample (OT2_cohort) Illumina HiSeq 2000;ILLUMINA 4
EGAD00001003368 RNAseq on Illumina HiSeq2000/2500 of PDO culture derived from colorectal cancer primary tumor sample (OT2_cohort) Illumina HiSeq 2000;ILLUMINA 1
EGAD00001003370 Whole-genome sequencing on Illumina HiSeq2000/2500 of Blood EDTA (OT2_cohort) Illumina HiSeq 2000;ILLUMINA 10
EGAD00001003384 Whole-exome sequencing on Illumina HiSeq2000/2500 of Patient-derived xenograft derived from colorectal cancer primary tumor sample (OT2_cohort) Illumina HiSeq 2000;ILLUMINA 14
EGAD00001003380 Whole-exome sequencing on Illumina HiSeq2000/2500 of PDO culture derived from colorectal cancer metastasis sample (OT2_cohort) Illumina HiSeq 2000;ILLUMINA 1
EGAD00001003456 There are 5WGS and 35WES sample pairs from the first affiliated hospital of kunming medical university, which belongs to ICGC projects COCA-CN. Illumina HiSeq 2000;ILLUMINA 80
EGAD00001003597 Promoter capture HiC on KMS11 (multiple myeloma) Illumina HiSeq 2000;ILLUMINA 1
EGAD00001003223 we collected tumor samples and adjacent nomal mucosae from 5 patients with colorectal cancer in surgical operation from 2014 to 2016 in the First Affiliated Hospital of Chongqing Medical University (Chongqing, China) and the Research Institute of Surgery, Third Military Medical University (Chongqing, China). the qualified captured library of each sample was then loaded on Illumina HiSeq 2000 (Illumina, San Diego, CA) platforms and subjected to high-throughput sequencing. Illumina HiSeq 2000;ILLUMINA 10
EGAD00001003596 The MITOEXME project aims to improve protocols for molecular diagnosis of patients with OXPHOS disorders with a focus on a next generation sequencing methods and to increase the knowledge of pahtophysiological mechanisms by identification of new targets and cellular studies. In this project we will sequence the exomes fo 120 patients. This dataset contains all the data available for this study on 2017-08-29. Illumina HiSeq 2000;ILLUMINA 125
EGAD00001003326 Azoospermia, characterized by the absence of spermatozoa in the ejaculate is a common cause of male infertility with a poorly characterized etiology. Exome sequencing analysis of two azoospermic brothers allowed the identification of a homozygous splice mutation in SPINK2, encoding a serine protease inhibitor believed to target acrosin, the main sperm acrosomal protease. In accord with these findings we observed that homozygous Spink2 KO male mice had azoospermia. Moreover, despite normal fertility, heterozygous male mice had a high rate of morphologically abnormal spermatozoa and a reduced sperm motility. Further analysis demonstrated that in the absence of Spink2, protease-induced stress initiates Golgi fragmentation and prevents acrosome biogenesis leading to spermatid differentiation arrest. We also observed a deleterious effect of acrosin overexpression in HEK cells, effect that was alleviated by SPINK2 coexpression confirming its role as acrosin inhibitor. These results demonstrate that SPINK2 is necessary to neutralize proteases during their cellular transit towards the acrosome and that its deficiency induces a pathological continuum ranging from oligoasthenoteratozoospermia in heterozygotes to azoospermia in homozygotes. Illumina HiSeq 2000;ILLUMINA 2
EGAD00001003458 Fastq data of genomics heterogeneity of multiple synchronous lung cancer. Whole-genome sequencing (WGS) were performed in 3 tumour samples, one regional lymph node metastasis sample and peripheral blood sample from the same patient with MSLCs. Illumina HiSeq 2000;ILLUMINA 6
EGAD00001003316 RNAseq of LC2AD with AD80 or DMSO Plenker et al., Mechanistic insight into RET kinase inhibitors targeting the DFG-out conformation in RET-rearranged cancer Illumina HiSeq 2000;ILLUMINA 1
EGAD00001003461 H3K27ac ChIP-seq and input genome sequencing was performed in 19 primary prostate tumours classified as intermediate risk. Sequencing of ChIP DNA was performed on an Illumina HiSeq 2000 as either single end 50 bp reads (for 7 samples) or paired end 100 bp reads (for 12 samples). Input DNA from all samples was sequenced using single-end 50 bp reads. The files provided are in fastq format. Illumina HiSeq 2000;ILLUMINA 27
EGAD00001003262 High-coverage WES sequencing of DNA samples from 50 PTCs was performed on the Illumina HiSeq 2500 or 4000 System Illumina HiSeq 2000;ILLUMINA 100
EGAD00001003452 The samples include paired tumor and normal tissues from 205 patients (201 for normal and primary tumor tissues; 4 for normal, primary tumor and liver metastatic tissues). High-coverage WES sequencing or whole genome sequencing of DNA samples were performed on the Illumina HiSeq 2000 system Illumina HiSeq 2000;ILLUMINA 30
EGAD00001003755 This dataset provides whole genome sequencing data of normal/tumors pairs from 9 patients with uterine or ovarian carcinosarcoma using the HiSeq 2000 sequencing system. It includes 27 samples (9 normals, 16 uterine tumors and 2 ovarian tumors). Through separate whole genome sequencing of carcinomatous and sarcomatoid components, we analyse and compare the genomic alterations of these components. Illumina HiSeq 2000;ILLUMINA 27
EGAD00001002401 RNA-Seq data for 14 Multiple Myeloma sample(s). 14 run(s), 14 experiment(s), 14 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816 Illumina HiSeq 2000;ILLUMINA 14
EGAD00001003760 There are 88 paired samples from HCC patients including tumors and matched adjacent normal tissues which were sequencing by Illumina HiSeq 2000 platform. Illumina HiSeq 2000;ILLUMINA 176
EGAD00001003563 Whole exome sequencing of diffuse intrinsic pontine glioma (DIPG) cells isolated from the pons and from a sub-ventricular zone site of spread within the frontal lobe from the same individual (SU- DIPG-XIII) Illumina HiSeq 2000;ILLUMINA 3 sample
EGAD00001003269 High-coverage WGS sequencing of DNA samples from 90pairs GCs was performed on the Illumina HiSeq X Ten System. Illumina HiSeq 2000;ILLUMINA 1,332
EGAD00001003551 The samples include paired tumor and normal tissues from 106 patients . High-coverage WES sequencing or whole genome sequencing of DNA samples were performed on the Illumina HiSeq 2000 system Illumina HiSeq 2000;ILLUMINA 212
EGAD00001003429 RNA analysis of two patients 11 and 15 with WGS done on Illumina HiSeq2000. For research purpose and authorised user only. Illumina HiSeq 2000;ILLUMINA 2
EGAD00001003438 Three files of patients 20, 23 and 25 with WGS done on Illumina HiSeq 2000. For research purpose and authorised user only. Illumina HiSeq 2000;ILLUMINA 3
EGAD00001003205 160 WES and 25 WGS for HBV related HCC, and 15 WES for ICC belongs LICA-CN Illumina HiSeq 2000;ILLUMINA 402
EGAD00001003464 For RNA-Seq total RNA was isolated following LDC67 or JQ1 treatment. 3’RNAseq libraries were prepared with QUANT SEQ FWD 3´mRNA-Seq Kit (Lexogen, Austria), sequenced on an Illumina HiSeq 4000 Illumina HiSeq 2000;ILLUMINA 3
EGAD00001003762 Whole Exome sequencing of paediatric High Grade Gliomas Illumina HiSeq 2000;ILLUMINA 100
EGAD00001000782 Whole-genome sequencing was performed by Illumina Inc (San Diego, CA). Libraries were constructed with ~300bp insert length and paired-end 100bp reads were sequenced on Illumina HiSeq2000. Illumina HiSeq 2000;ILLUMINA 190
EGAD00001003208 Whole genome sequencing data for MMML (12 tumor/control pairs) Illumina HiSeq 2000;ILLUMINA 25
EGAD00001003344 Transcriptome profiling of 25 prostate tumor samples by RNA-Seq Illumina HiSeq 2000;ILLUMINA 25
EGAD00001003745 Exome sequencing fastq files from 6 mutation carriers and 5 non-carriers from 2 families. One µg DNA was used for library preparation using the TruSeq DNA LT Sample Prep Kit v2 according to the manufacturer’s instructions (Illumina). Hybridization was performed using Nimblegen SeqCap EZ Exome v3 (Roche) and Paired-end Sequencing (2x100 bp) on the Illumina HiSeq 2000 with TruSeq v3 chemistry (Illumina). Illumina HiSeq 2000;ILLUMINA 11
EGAD00001003782 When available (25 primary MDS, 12 MDS/MPN, and 6 AML-MRC cases), high quality RNA (stranded-total) was submitted for RNA-seq. RNA was extracted from bulk myeloid cells which was used as the tumor population. Files uploaded are mapped BAM files. Illumina HiSeq 2000;ILLUMINA 43
EGAD00001003435 Whole Genome Sequencing for the paper titled "Orthotopic Patient-Derived Xenografts of Pediatric Solid Tumors" Illumina HiSeq 2000;ILLUMINA 150
EGAD00001003434 Whole Exome Sequencing for the paper titled "Orthotopic Patient-Derived Xenografts of Pediatric Solid Tumors" Illumina HiSeq 2000;ILLUMINA 149
EGAD00001003433 RNA-Seq data for the paper titled "Orthotopic Patient-Derived Xenografts of Pediatric Solid Tumors" Illumina HiSeq 2000;ILLUMINA 95
EGAD00001003781 Paired whole exome sequencing for 32 primary MDS, 14 MDS/MPN, and 8 AML-MRC cases (total = 54). Normal comparator genomic DNA was extracted from lymphocytes purified by flow cytometry. Bulk myeloid cells were used as a source of tumor gDNA. Files uploaded are mapped BAM files. Illumina HiSeq 2000;ILLUMINA 94
EGAD00001003789 Exome reads constituting of FASTQ paired end reads from 5 FHD/FHDL patients Illumina HiSeq 2000;ILLUMINA 16
EGAD00001003790 RNA seq reads constituting of FASTQ paired end reads from 5 FHD/FHDL patients Illumina HiSeq 2000;ILLUMINA 13
EGAD00001003787 BBMRI - BIOS project - Freeze 2 - Fastq files - GoNL samples Illumina HiSeq 2000;ILLUMINA 420
EGAD00001003784 BBMRI - BIOS project - Freeze 2 - Bam files - unrelated samples Illumina HiSeq 2000;ILLUMINA 3,559
EGAD00001003786 BBMRI - BIOS project - Freeze 2 - Bam files - GoNL samples Illumina HiSeq 2000;ILLUMINA 420
EGAD00001003785 BBMRI - BIOS project - Freeze 2 - Fastq files - unrelated samples Illumina HiSeq 2000;ILLUMINA 3,559
EGAD00001003757 BBMRI - BIOS project - Freeze 2 - Fastq files Illumina HiSeq 2000;ILLUMINA 3,686
EGAD00001003758 BBMRI - BIOS project - Freeze 2 - Bam files Illumina HiSeq 2000;ILLUMINA 3,686
EGAD00001003778 Illumina HiSeq 2000;ILLUMINA 1
EGAD00001001011 Monocyte differentiation into macrophages represents a cornerstone process for host defense. Concomitantly, immunological imprinting of either tolerance or trained immunity determines the functional fate of macrophages and susceptibility to secondary infections. Transcriptomes (RNA-Seq) and epigenomes (ChIP-Seq H3K4me1,H3K4me3,H3K27ac) in four primary cell types: monocytes, in vitro differentiated naive, tolerized and trained macrophages were characterized. Inflammatory and metabolic pathways were modulated in macrophages, including decreased inflammasome activation, and pathways functionally implicated in trained immunity were identified. Strikingly, B-glucan training elicits an exclusive epigenetic signature, revealing a complex network of enhancers and promoters. Analysis of transcription factor motifs in DNase I hypersensitive sites at cell-type specific epigenetic loci unveiled differentiation and treatment specific repertoires. Altogether, this study provides a resource to understand the epigenetic changes that underlie innate immunity in humans. Illumina HiSeq 2000;, NextSeq 500; 57 fastq
EGAD00001001197 ChIP-Seq data for 2 monocyte sample(s). 7 run(s), 7 experiment(s), 7 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000;, NextSeq 500; 2 fastq,bam
EGAD00001001196 ChIP-Seq data for 13 macrophage sample(s). 55 run(s), 55 experiment(s), 55 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000;, NextSeq 500; 13 fastq,readme_file,bam
EGAD00001001576 ChIP-Seq data for 12 macrophage sample(s). 49 run(s), 49 experiment(s), 49 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820 Illumina HiSeq 2000;, NextSeq 500; 12 fastq,bam
EGAD00001001580 ChIP-Seq data for 2 monocyte sample(s). 6 run(s), 6 experiment(s), 6 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820 Illumina HiSeq 2000;, NextSeq 500; 2 fastq,bam
EGAD00001002454 ChIP-Seq data for 4 band form neutrophil sample(s). 26 run(s), 23 experiment(s), 23 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;, NextSeq 500; 4 bam,fastq
EGAD00001002491 ChIP-Seq data for 2 monocyte - T=0days sample(s). 7 run(s), 7 experiment(s), 7 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;, NextSeq 500; 2 bam,fastq
EGAD00001002458 ChIP-Seq data for 2 macrophage - T=6days untreated sample(s). 6 run(s), 6 experiment(s), 6 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;, NextSeq 500; 2 bam,fastq
EGAD00001002498 ChIP-Seq data for 2 macrophage - T=6days LPS sample(s). 6 run(s), 6 experiment(s), 6 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816 Illumina HiSeq 2000;, NextSeq 500; 2 bam,fastq
EGAD00001000734 Paired end Illumina sequencing of whole exomes of multiple tumour regions. Illumina HiSeq 2000;, Illumina HiSeq 2500;, Illumina Genome Analyzer IIx; 88 bam
EGAD00001000371 Sequencing data for PDAC cell lines generated by QCMG Illumina HiSeq 2000;, Illumina HiSeq 2500; 54 bam
EGAD00001001444 Atypical teratoid/rhabdoid tumor (ATRT) is one of the most common brain tumors in infants and young children. Although the prognosis of ATRT patients is poor, some patients respond very well to current treatments, suggesting inter-tumor molecular heterogeneity. To investigate this further, we genetically and epigenetically analyzed a large cohort of ATRTs (n = 170). Three distinct molecular subgroups of ATRTs, associated with differences in demographics, tumor location and type of SMARCB1 alterations, were identified using DNA-methylation or gene expression analyses. Whole genome DNA- and RNA-sequencing found no other recurrent mutations explaining the differences between subgroups. However, whole genome bisulfite-sequencing and H3K27Ac ChIP-sequencing of primary tumors revealed clear differences in methylation patterns and enhancer landscapes, leading to the identification of subgroup-specific regulatory networks. Illumina HiSeq 2000;, Illumina HiSeq 2500; 55 fastq
EGAD00001001312 Fastq data for whole genome bisulfite sequencing assays for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2000;, Illumina HiSeq 2500; 30 fastq
EGAD00001001095 Supporting data for ICGC PACA-CA Release 18 Illumina HiSeq 2000;, Illumina HiSeq 2500; 506 bam,fastq
EGAD00001001424 We obtained paired longitudinal specimens from a total of 38 glioblastoma (GBM) patients (34 primary and 4 secondary GBM patients). Treatment-naive initial tumors were available for 35 cases; for the other 3 cases, we used the first available recurrent tumors in lieu of initial tumors. Tumor specimens were subjected to whole-exome sequencing (27 of 38 cases, with the matched normal/blood for 22 of the 27 cases) and transcriptome sequencing (30 of 38 cases). Illumina HiSeq 2000;, Illumina HiSeq 2500; 141 bam
EGAD00001001608 Aligned BAM files of whole exome sequencing of 20 syCRCs and 10 normal counterparts. Each sample of 4 patients (S13, S3, S12 and S6) underwent two sequencing rounds. Illumina HiSeq 2000;, Illumina HiSeq 2500; 42 bam
EGAD00001001441 Despite the established role of the transcription factor MYC in cancer, little is known about the impact of a new class of transcriptional regulators, the long non-coding RNAs (lncRNAs), on the way MYC is able to influence cellular transcriptome. To this aim we have intersected RNA-sequencing data from two MYC-inducible cell lines and from a cohort of 91 mature B-cell lymphomas carrying, or not carrying, genetic variants resulting in MYC over-expression. By this approach, we identified 13 lncRNAs differentially expressed in IG-MYC-positive Burkitt lymphoma and regulated in the same direction by MYC in the model cell lines. Among them we focused on a lncRNA that we named MINCR, for MYC-Induced long Non-Coding RNA, showing a strong correlation with MYC expression in MYC-positive lymphomas and also in pancreatic ductal adenocarcinomas. To understand its cellular role we performed RNA interference (RNAi) experiments and found that MINCR knock-down is associated with a reduction in cellular viability, due to an impairment in cell cycle progression. Differential gene expression analysis following RNAi showed a strongly significant enrichment of cell cycle genes among the genes down-regulate following MINCR knock-down. Interestingly these genes are enriched in MYC binding sites in their promoters, suggesting that MINCR acts as a modulator of MYC transcriptional program. Accordingly, following MINCR knock-down, we observed a reduction in the binding of MYC to the promoters of selected cell cycle genes. Finally we provide evidences that down-regulation of AURKA, AURKB and CTD1 may explain the reduction in cellular proliferation observed upon MINCR knock-down. We therefore suggest that MINCR is a newly identified player in the MYC transcriptional network able to control the expression of cell cycle genes. Illumina HiSeq 2000;, Illumina HiSeq 2500; 49 fastq
EGAD00001001119 Whole Genome Bisulfite Sequencing Illumina HiSeq 2000;, Illumina HiSeq 2500; 26 fastq
EGAD00001001120 Whole Genome Sequencing Illumina HiSeq 2000;, Illumina HiSeq 2500; 64 fastq
EGAD00001001595 ICGC PACA-CA Release 20 Illumina HiSeq 2000;, Illumina HiSeq 2500; 516 bam,fastq
EGAD00001001321 This dataset includes WGS & WTS alignment data generated from 1 ATC tumor, its matched peripheral blood specimen and 3 authenticated ATC cell lines, THJ-16T, THJ-21T and THJ-29T. In addition, it includes WTS data from extra 4 unique anaplastic cell lines, ACT-1, C643, HTh7 and T238. Illumina HiSeq 2000;, Illumina HiSeq 2500; 13 bam
EGAD00001001618 Sequence data from two medullary thyroid carcinoma patients: WGS datasets generated from tumors and matched normal tissues and RNA-Seq from tumors are included. Illumina HiSeq 2000;, Illumina HiSeq 2500; 6 bam
EGAD00001002173 A KNIH007 mRNA-seq paired end data for adipocytes Illumina HiSeq 2000;, Illumina HiSeq 2500; 1 fastq
EGAD00001000994 HIPO blastemal Wilms (nephroblastoma) characterisation of tumor driving chromosomal aberrations Illumina HiSeq 2000;, Illumina HiSeq 2500; 56 fastq
EGAD00001001973 Exome sequencing of 184 samples from consanguineous families with different congenital heart defects collected at KAIMRC, Riyadh, Saudi Arabia. Illumina HiSeq 2000;, Illumina HiSeq 2500; 179 cram
EGAD00001000791 Exome sequencing of familial and sporadic small cell cancer of ovary cases. Illumina HiSeq 2000;, Illumina HiSeq 2500; 16 fastq
EGAD00001001462 Exome sequencing of 142 samples with corresponding Sanger sequencing results for 409 variants and 321 negative sites. DNA library preps prepared with Illumina TruSeq sample preparation kit. The captured DNA libraries were PCR amplified using the supplied paired-end PCR primers. Sequencing was performed with an Illumina HiSeq2000 (SBS Kit v3, one pool per lane) generating 2x101-bp reads. Illumina HiSeq 2000;, Illumina HiSeq 2500; 142 fastq
EGAD00001001998 This dataset consists of sequencing data on 15 patients with Sezary syndrome. On 12 of these patients, we have exome sequencing data while on 10 patients, we have RNA sequencing data. In total for seven patients, we have both exome as well as RNA sequencing data. We looked for gene mutations and fusion events in these patients to identify genes that could be involved in the pathogenesis of the disease. Illumina HiSeq 2000;, Illumina HiSeq 2500; 30 fastq
EGAD00001001956 ICGC Release 21 for PACA-CA from OICR Illumina HiSeq 2000;, Illumina HiSeq 2500; 516 fastq,bam
EGAD00001002186 Around 10% of patients who present in melanoma clinics have a first degree relative with a previous diagnosis of melanoma. While around 3% have three or more relatives who have been diagnosed with the disease. In this project we will whole genome sequence patients from large Dutch familial melanoma pedigrees to identify mutations in genes that drive melanomagenesis. The identification of these genes will facilitate the management of familial melanoma patients and their families. Illumina HiSeq 2000;, Illumina HiSeq 2500; 38 cram
EGAD00001002135 ChIPseq data of Atypical teratoid/rhabdoid tumors (ATRT) Illumina HiSeq 2000;, Illumina HiSeq 2500; 15 fastq
EGAD00001002205 The BLUEPRINT project is a large-scale project investigating epigenetic mechanisms involved in blood formation, in health and disease. The human variation workpackage (WP10, led by NS) of the project seeks to characterize the effect of common sequence variation on the epigenome status of a cell. To do this, the project will use highly purified blood cells to minimise "experimental noise" and therefore enhance the power to discover modest effects. Two peripheral blood cell types, the CD14+CD16- monocyte (an important central orchestrator of adaptive immunity and a bridge between innate and adaptive immunity) and the CD65+CD9- neutrophilic granulocyte (the frontline cell for innate immunity) have been selected for this purpose. The two types of cells will be obtained at high purity from adult blood (AB) of 200 healthy males and females, respectively. Cells will be purified by using already validated and fully operational protocols that are based on density gradient centrifugation of the buffy coat obtained from whole blood, followed by magnetic bead-based purification using monoclonal antibodies against Cluster of Differentiation (CD) lineage-specific cell surface markers. Units of 475 ml of AB will be obtained from consenting volunteers of the Cambridge BioResource (CBR), a panel of 10,000 healthy volunteers local to Cambridge who have already consented to participate in biomedical research and of whom biological samples (DNA, plasma, serum) and lifestyle data have been deposited in a repository and database, respectively. We are requesting funding from the Human Diversity project to sequence the genomes of the 200 CBR volunteers at low pass (6x coverage). Nuclei, DNA and RNA will be recovered from the purified cells and made available for RNA-seq, DNA-seq and ChIP-seq and genomic DNA for entire genome sequencing will be recovered from the DNA repository. Illumina HiSeq 2000;, Illumina HiSeq 2500; 155 cram
EGAD00001001208 Targeted capture of cancer gene panel bait set in single cell derived organoids from colon tissue and colorectal cancer from 1 patient. Illumina HiSeq 2000;, Illumina HiSeq 2500; 105 cram
EGAD00001001673 Part of WGS seq data of Maligant Lymphoma study (ICGC) Illumina HiSeq 2000;, Illumina HiSeq 2500; 112 readme_file,fastq
EGAD00001002263 This is the first dataset for the Botseq sequencing project Illumina HiSeq 2000;, Illumina HiSeq 2500; 39 bam
EGAD00001000176 DATA_SET_Comparing_sequencing_four_proto-typical_Burkitt_lymphomas_BL_IG-MYC_translocation Illumina HiSeq 2000;, Illumina Genome Analyzer IIx; 8 bam
EGAD00001000327 release_2: ICGC PedBrain: whole genome mate-pair sequencing Illumina HiSeq 2000;, Illumina Genome Analyzer IIx; 70 bam,fastq
EGAD00001000282 Neuroblastomas are tumors of peripheral sympathetic neurons and are the most common solid tumor in children. To determine the genetic basis for neuroblastoma we performed whole-genome sequencing (6 cases), exome sequencing (16 cases), genome-wide rearrangement analyses (32 cases), and targeted analyses of specific genomic loci (40 cases) using massively parallel sequencing. On average each tumor had 19 somatic alterations in coding genes (range, 3-70). Among genes not previously known to be involved in neuroblastoma, chromosomal deletions and sequence alterations of chromatin remodeling genes, ARID1A and ARID1B, were identified in 8 of 71 tumors (11%) and were associated with early treatment failure and decreased survival. Using tumor-specific structural alterations, we developed an approach to identify rearranged DNA fragments in sera, providing personalized biomarkers for minimal residual disease detection and monitoring. These results highlight dysregulation of chromatin remodeling in pediatric tumorigenesis and provide new approaches for the management of neuroblastoma patients. Illumina HiSeq 2000;, Illumina Genome Analyzer IIx; 114 fastq
EGAD00001000628 Illumina HiSeq 2000;, Illumina Genome Analyzer IIx; 66 bam
EGAD00001000697 Illumina HiSeq sequence data (with >30x coverage) were aligned to the hg19 human reference genome assembly using BWA (Li and Durbin, 2009); duplicate reads were removed from the final BAM file. No realignment or recalibration was performed. Illumina HiSeq 2000;, Illumina Genome Analyzer IIx; 90 bam
EGAD00001000873 Fastq files of 10 samples of condrosarcoma Illumina HiSeq 2000;, Illumina Genome Analyzer IIx; 10 fastq
EGAD00001000808 RIKEN collection WGS reads for 321 HCC and blood matched samples from 158 donors submitted to ICGC for release 15 Illumina HiSeq 2000;, Illumina Genome Analyzer IIx; 321 fastq
EGAD00001000882 Targeted genome sequences of the human X chromosome in 4 colorectal adenomas and 4 matched normal tissues from male patients Illumina HiSeq 2000;, Illumina Genome Analyzer IIx; 8 bam
EGAD00001001262 Unaligned bam of 31 samples derived from primary tumor Illumina HiSeq 2000;, Illumina Genome Analyzer IIx; 31 bam
EGAD00001001002 Exome sequencing data for 8 pairs of seminomas and matched normal Illumina HiSeq 2000;, Illumina Genome Analyzer IIx; 16 fastq
EGAD00001001035 RIKEN collection WGS and RNA-seq reads for 66 HBV-associated HCC and matched blood or liver samples from 22 donors. Illumina HiSeq 2000;, Illumina Genome Analyzer IIx; 66 fastq
EGAD00001001625 release_2: ICGC PedBrain: whole genome sequencing Illumina HiSeq 2000;, Illumina Genome Analyzer IIx; 209 bam,fastq
EGAD00001001881 RIKEN collection of WGS reads for 543 liver cancer and matched blood or liver samples from 260 donors. Illumina HiSeq 2000;, Illumina Genome Analyzer IIx; 543 fastq
EGAD00001001880 RIKEN collection of RNA-seq reads for 458 liver cancer samples and matched normal liver from 247 donors. Illumina HiSeq 2000;, Illumina Genome Analyzer IIx; 458 fastq
EGAD00001001412 Whole genome sequencing of 48 tumor/normal pairs obtained from adult T-cell leukemia/lymphoma. This data set includes 11 full-pass WGS and 37 low-pass WGS data. Illumina HiSeq 2000;, HiSeq X Ten; 96 bam
EGAD00001000227 EGAD00001000227_UK10K_NEURO_ABERDEEN_REL_2012_07_05 Illumina HiSeq 2000; 347 vcf
EGAD00001000315 UK10K_NEURO_ABERDEEN REL-2012-11-27 Illumina HiSeq 2000; 313 vcf
EGAD00001000271 Pilot study Pilocytic Astrocytoma ICGC PedBrain, whole genome sequencing of 5 tumors and matched blood Illumina HiSeq 2000; 10 bam
EGAD00001000887 Exome sequencing of Resistant BCC samples. Illumina HiSeq 2000; 23 fastq
EGAD00001000881 RNA sequencing of Resistant BCC samples. Illumina HiSeq 2000; 11 fastq
EGAD00001000269 OLD DATA FILES FOR SJMB - Superseded by EGAD00001001864 Illumina HiSeq 2000; 68 bam
EGAD00001000319 UK10K_NEURO_GURLING REL-2012-11-27 Illumina HiSeq 2000; 48 vcf
EGAD00001000237 EGAD00001000237_UK10K_NEURO_GURLING_REL_2012_07_05 Illumina HiSeq 2000; 43 vcf
EGAD00001000336 UK10K_OBESITY_SCOOP REL-2012-11-27 Illumina HiSeq 2000; 784 vcf
EGAD00001000241 EGAD00001000241_UK10K_OBESITY_SCOOP_REL_2012_07_05 Illumina HiSeq 2000; 674 vcf
EGAD00001000151 UK10K OBESITY REL-2011-07-14 Illumina HiSeq 2000; 88 vcf
EGAD00001000181 UK10K_OBESITY_SCOOP REL-2012-01-13 Illumina HiSeq 2000; 212 vcf
EGAD00001000193 UK10K_OBESITY_SCOOP REL-2012-02-22 Illumina HiSeq 2000; 573 vcf
EGAD00001000318 UK10K_NEURO_FSZ REL-2012-11-27 Illumina HiSeq 2000; 119 vcf
EGAD00001000184 UK10K_NEURO_FSZ_REL_2012_01_13 Illumina HiSeq 2000; 120 vcf
EGAD00001000240 UK10K_NEURO_FSZ_REL_2012_07_05 Illumina HiSeq 2000; 120 vcf
EGAD00001000215 RNA sequencing of colon tumor/normal sample pairs Illumina HiSeq 2000; 139 fastq
EGAD00001000216 Exome capture sequencing of colon tumor/normal pairs Illumina HiSeq 2000; 144 fastq
EGAD00001000214 Whole genome sequencing of colon samples Illumina HiSeq 2000; 11 fastq
EGAD00001000306 ICGC prostate cancer whole genome sequencing Illumina HiSeq 2000; 22 bam
EGAD00001000270 DATA_SET_EOP-PCA-LargeAndSmallTumors1 Illumina HiSeq 2000; 18 bam
EGAD00001000235 EGAD00001000235_UK10K_NEURO_IOP_COLLIER_REL_2012_07_05 Illumina HiSeq 2000; 170 vcf
EGAD00001000321 UK10K_NEURO_IOP_COLLIER REL-2012-11-27 Illumina HiSeq 2000; 158 vcf
EGAD00001002158 This is an in vitro genome-wide CRISPR/cas9 screen in human glioblastoma stem cells, screening for genes essential for survival of these cells. These cells express cas9 and have been transfected with a guide RNA library causing gene knockouts. We will analyse the sequencing data for depletion of guide RNAs. This dataset contains all the data available for this study on 2016-06-02. Illumina HiSeq 2000; 6 cram
EGAD00001000345 Exome sequencing of 12 DNA samples obtained from patients with structural brain malformations. Illumina HiSeq 2000; 9 bam
EGAD00001000310 UK10K_NEURO_ASD_BIONED REL-2012-11-27 Illumina HiSeq 2000; 76 vcf,bam
EGAD00001000228 EGAD00001000228_UK10K_NEURO_ASD_BIONED_REL_2012_07_05 Illumina HiSeq 2000; 59 vcf
EGAD00001001125 Exome sequencing of Untreated BCC samples. Illumina HiSeq 2000; 91 fastq
EGAD00001000261 Retinoblastoma whole genome sequencing Illumina HiSeq 2000; 8 bam
EGAD00001000256 UK10K_NEURO_UKSCZ REL-2012-07-05 Illumina HiSeq 2000; 595 vcf
EGAD00001000335 UK10K_NEURO_UKSCZ REL-2012-11-27 Illumina HiSeq 2000; 527 vcf
EGAD00001000182 UK10K_NEURO_UKSCZ REL-2012-01-13 Illumina HiSeq 2000; 95 vcf
EGAD00001000317 UK10K_NEURO_EDINBURGH REL-2012-11-27 Illumina HiSeq 2000; 214 vcf
EGAD00001000233 EGAD00001000233_UK10K_NEURO_EDINBURGH_REL_2012_07_05 Illumina HiSeq 2000; 219 vcf
EGAD00001000383 In collaboration with Dr Robert Semple we have identified a family harbouring an autosomal dominant variant, which leads to severe insulin resistance (SIR), short stature and facial dysmorphism. This family is unique within the SIR cohort in having normal lipid profiles, preserved adiponectin and normal INSR expression and phosphorylation. DNA is available for 7 affected and 7 unaffected family members across 3 generations. All 14 samples have been genotyped using microsatellites and the Affymetrix 6.0 SNP chip. Linkage analysis identified an 18.8Mb haplotype on chromosome 19 as a possible location of the causative variant. However, Exome sequencing of 3 affected and 1 unaffected family members has not identified the causative variant suggesting the possibility of an intronic or intergenic variant in this region or elsewhere in the genome. We propose to conduct whole genome sequencing of 5 members of the pedigree at a depth of 20X. The chosen samples are two sets of parents plus one member of an unaffected branch of the pedigree who shares the risk haplotype on chromosome 19. Sequencing of the two sets of parents will be used along with the genome-wide SNP data to impute 4 affected children giving an effect sample size of 6 affected individuals. Illumina HiSeq 2000; 7 bam
EGAD00001000347 These samples include exome sequences of family members with dyslipidemias from Finnish origin. Illumina HiSeq 2000; 95 bam
EGAD00001001862 RNA-seq of PDXs Illumina HiSeq 2000; 12 fastq
EGAD00001001693 Fastq files of RNAseq of 182 samples of biliary tract cancer Illumina HiSeq 2000; 182 fastq
EGAD00001001872 Targeted exome sequencing of patient derived xenografts from primary colorectal tumours and liver metastases. This dataset contains all the data available for this study on 2016-01-06. Illumina HiSeq 2000; 333 cram
EGAD00001001873 AML emerges as a consequence of accumulating independent genetic aberrations that direct regulation and/or dysfunction of genes resulting in aberrant activation of signalling pathways, resistance to apoptosis and uncontrolled proliferation. Given the significant heterogeneity of AML genomes, AML patients demonstrate a highly variable response rate and poor median survival in response to current chemotherapy regimens. For the past 4 years we have conducted gene expression profiling on purified bone marrow populations equating to normal haematopoietic stem and progenitor cells from healthy subjects and patients with de novo AML in order to identify AML signatures of aberrantly expressed genes in cancer versus normal. We are now applying a series of bioinformatic methodologies combined with clinical and conventional diagnostic data to establish novel genomics strategies for improved prognostication of AML. Additionally, we use our AML signatures to unravel oncogenic signalling pathway activities in AML patients and test inhibitory drugs for these pathways inn preclinical therapeutic programmes. We consider that superimposing GEP and clinical data for our AML patient cohort with additional data on their mutational status will significantly improve the prognostic power of the study as well as unravel yet unknown mutations associated with aberrant signalling activities of oncogenic pathways. Illumina HiSeq 2000; 215 cram
EGAD00001000390 We propose to definitively characterise the somatic genetics of triple negative breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. Illumina HiSeq 2000; 101 bam,cram
EGAD00001000444 Cancer is driven my mutations in the genome. We will uncover the mutations that give rise to Ewing's sarcoma, a bone tumour that largely affects children. We will use second generation Illumina massively parallel sequencing, and bespoke software, to characterise the genomes and transcriptomes of Ewing's sarcoma tumours. Illumina HiSeq 2000; 3 bam
EGAD00001000223 RNA sequencing of SCLC tumor/normal sample pairs and cell lines Illumina HiSeq 2000; 79 fastq
EGAD00001000222 Exome capture sequencing of SCLC tumor/normal pairs and cell lines Illumina HiSeq 2000; 103 fastq
EGAD00001000221 Whole genome sequencing of SCLC tumor/normal samples Illumina HiSeq 2000; 4 fastq
EGAD00001001053 DATA FILES FOR SJOS-WGS-2ndBatch Illumina HiSeq 2000; 27 bam
EGAD00001001052 DATA FILES FOR SJTALL Illumina HiSeq 2000; 24 bam
EGAD00001000259 DATA FILES FOR SJAMLM7 Illumina HiSeq 2000; 8 bam
EGAD00001000183 UK10K_NEURO_FSZNK REL-2012-01-13 Illumina HiSeq 2000; 273 vcf
EGAD00001000234 EGAD00001000234_UK10K_NEURO_FSZNK_REL_2012_07_05 Illumina HiSeq 2000; 281 vcf
EGAD00001000332 UK10K_NEURO_FSZNK REL-2012-11-27 Illumina HiSeq 2000; 258 vcf
EGAD00001000382 Whole Exome Sequencing of Permanent Neonatal Diabetes Patients Illumina HiSeq 2000; 25 bam
EGAD00001000232 EGAD00001000232_UK10K_NEURO_ASD_TAMPERE_REL_2012_07_05 Illumina HiSeq 2000; 54 vcf
EGAD00001000314 UK10K_NEURO_ASD_TAMPERE REL-2012-11-27 Illumina HiSeq 2000; 48 vcf
EGAD00001000343 This project aims to identify highly penetrant coding variants increasing the risk of Congenital Heart Disease (CHD) performing whole exome sequencing on DNA samples from 23 affected individuals, selected from 10 families with presumed Autosomal Recessive Inheritance. This is a collaboration with Prof. Eamonn Maher and Dr. Chirag Patel from the Department of Medical and Molecular Genetics, University of Birmingham plans to sequence 23 indexed Agilent whole exome pulldown libraries on 75Bp PE HiSeq (Illumina) Illumina HiSeq 2000; 24 bam
EGAD00001000249 This is the bam file generated after alignment using BWA program for the SAIF genome Illumina HiSeq 2000; 1 bam
EGAD00001000254 This dataset contain the raw files generated for SAIF genome project Illumina HiSeq 2000; 1 fastq
EGAD00001000381 Illumina paired-end sequencing of whole- exome pulldown DNA from Severe Insulin Resistant patients. Illumina HiSeq 2000; 3 bam
EGAD00001000602 Illumina HiSeq 2000; 1 bam
EGAD00001000358 Chondrosarcoma (CHS) is a heterogeneous collection of malignant bone tumours and is the second most common primary malignancy of bone after osteosarcoma. Recent work has identified frequent, recurrent mutations in IDH1/2 in nearly half of central CHS. However, there has been little systematic genomic analysis of this tumour type and thus the contribution of other genes is unclear. Here we report comprehensive genomic analyses of 49 cases of CHS. We identified hypermutability of the major cartilage collagen COL2A1 with insertions, deletions and rearrangements identified in 37% of cases. The patterns of mutation were consistent with selection for variants likely to impair normal collagen biosynthesis. In addition we identified mutations in IDH1/2 (59%), TP53 (20%), the RB1 pathway (27%) and hedgehog signaling (22%). Illumina HiSeq 2000; 17 bam
EGAD00001000229 EGAD00001000229_UK10K_NEURO_ASD_FI_REL_2012_07_05 Illumina HiSeq 2000; 85 vcf
EGAD00001000173 UK10K_NEURO_ASD_FI REL-2012-01-13 Illumina HiSeq 2000; 85 vcf
EGAD00001000311 UK10K_NEURO_ASD_FI REL-2012-11-27 Illumina HiSeq 2000; 84 vcf
EGAD00001000231 EGAD00001000231_UK10K_NEURO_ASD_SKUSE_REL_2012_07_05 Illumina HiSeq 2000; 320 vcf
EGAD00001000313 UK10K_NEURO_ASD_SKUSE REL-2012-11-27 Illumina HiSeq 2000; 305 vcf
EGAD00001000280 This experiment is to validate putative somatic substitutions and indels identified in an exome screen of ~50 osteosarcoma tumour/normal pairs. It is the first stage in our ICGC commitment to study osteosarcoma. The validation process is an important component of our analysis to clarify the data prior to looking for evidence of new cancer genes, or subverted pathways important in the development of cancer. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina HiSeq 2000; 112 bam
EGAD00001000278 ICGC MMML-seq Data Freeze November 2012 whole genome sequencing Illumina HiSeq 2000; 12 bam
EGAD00001000281 ICGC MMML-seq Data Freeze November 2012 transcriptome sequencing Illumina HiSeq 2000; 6 bam
EGAD00001000356 ICGC MMML-seq Data Freeze March 2013 transcriptome sequencing Illumina HiSeq 2000; 23 bam
EGAD00001000355 ICGC MMML-seq Data Freeze March 2013 whole genome sequencing Illumina HiSeq 2000; 46 bam
EGAD00001000298 UK10K_RARE_NEUROMUSCULAR REL-2012-11-27 Illumina HiSeq 2000; 130 vcf
EGAD00001000180 UK10K_RARE_NEUROMUSCULAR REL-2012-01-13 Illumina HiSeq 2000; 47 vcf
EGAD00001000189 UK10K_RARE_NEUROMUSCULAR REL-2012-02-22 Illumina HiSeq 2000; 86 vcf
EGAD00001000219 UK10K_RARE_NEUROMUSCULAR REL-2012-07-05 Illumina HiSeq 2000; 117 vcf
EGAD00001000274 DATA_SET_TRANSCIPTOME_Comparing_sequencing_four_proto-typical_Burkitt_lymphomas_BL_IG-MYC_translocation Illumina HiSeq 2000; 4 bam
EGAD00001000359 In this study we will sequence the transcriptome of Verified Cancer Cell lines. This will be married up to whole exome and whole genome sequencing data to establish a full catalog of the variations and mutations found. Illumina HiSeq 2000; 2 bam
EGAD00001000393 Illumina HiSeq 2000; 30 vcf
EGAD00001000363 Common variable immunodeficiency (CVID) is the most common form of primary immunodeficiency with an estimated incidence of 1:10,000. It has been apparent for many years that CVID has a genetic component, occurs frequently in families and can have both a recessive or dominant mode of inheritance. In recent years, 4 genes underlying CVID have been identified; however, mutations within in them are estimated to account for no more than 10% of all cases of CVID. We have identified a multi-generational family with autosomal dominant CVID. Genome-wide linkage analysis has mapped the locus underlying CVID in this family to an approximately 9.2 Mb interval on chromosome 3q27.3-q29, between the markers D3S3570 and D3S1265. This locus is distinct from any of the previously mapped susceptibility loci suggesting a novel genetic variant is responsible for disease in this family. The aim of this study is to use exome sequencing of affected (n = 4) and unaffected (n = 4) individuals, in tandem with the available genetic mapping data, to identify the causal variant underlying CVID in this family. Illumina HiSeq 2000; 8 bam
EGAD00001000320 UK10K_NEURO_IMGSAC REL-2012-11-27 Illumina HiSeq 2000; 111 vcf
EGAD00001000239 EGAD00001000239_UK10K_NEURO_IMGSAC_REL_2012_07_05 Illumina HiSeq 2000; 114 vcf
EGAD00001000653 This is a continuation of the Chordoma Sequencing Project. All cancers arise due to somatically acquired abnormalities in DNA sequence. Systematic sequencing of cancer genomes allows acquisition of complete catalogues of all classes of somatic mutation present in cancer. These mutation catalogues will allow identification of the somatically mutated cancer genes that are operative and characterise patterns of somatic mutation that may reflect previous exogenous and endogenous mutagenic exposures. In this application, we aim to perform whole genome sequencing on 10 chordoma matched genome pairs. RNA Sequencing/Methylation and SNP6 and an additional sequencing of three cancer cell lines will be added to this work. Illumina HiSeq 2000; 10 bam,cram
EGAD00001000268 DATA FILES FOR SJCBF Illumina HiSeq 2000; 34 bam
EGAD00001000346 Exome sequencing of patients and their families with diverse rare neurological disorders. Some families have prior linkage data identifying a specific chromosomal interval or interest, other families do not have linkage data available. Many of these families come from special populations whose demography or preference for consanguineous marriages make them particularly tractable for genetic studies. Illumina HiSeq 2000; 30 bam
EGAD00001000352 DATA FILES FOR SJLGG Illumina HiSeq 2000; 7 bam
EGAD00001000353 DATA FILES FOR SJLGG Illumina HiSeq 2000; 45 bam
EGAD00001000344 Exome sequencing of 30 parent-offspring trios to >50X mean depth, where the offspring has sporadic TOF, to identify potential causal de novo mutations. We will use the exome plus design for pulldown that incorporates ~6.8Mb of additional regulatory sequences in addition to the ~50Mb GENCODE exome. Illumina HiSeq 2000; 90 bam
EGAD00001000341 This pilot study aims to generate pilot data to inform future study designs in consanguineous families or inbred populations by resequencing the exome of six individuals from five families with neurodevelopmental diseases. For all of these families a single mapping interval containing the causal variant has previously been identified. Illumina HiSeq 2000; 6 bam
EGAD00001000299 Whole exome sequencing of samples selected from the Finrisk sample collection. The samples sequenced in this study have all been collected in Kuusamo, Finland. Illumina HiSeq 2000; 24 bam
EGAD00001000242 EGAD00001000242_UK10K_NEURO_ASD_MGAS_REL_2012_07_05 Illumina HiSeq 2000; 60 vcf
EGAD00001000312 UK10K_NEURO_ASD_MGAS REL-2012-11-27 Illumina HiSeq 2000; 96 vcf
EGAD00001000328 ICGC PedBrain: RNA sequencing Illumina HiSeq 2000; 28 fastq
EGAD00001000275 Data set for Whole-genome-Sequencing of adult medulloblastoma Illumina HiSeq 2000; 10 bam
EGAD00001000248 RNAseq Pulldown Illumina HiSeq 2000; 6 bam
EGAD00001000230 EGAD00001000230_UK10K_NEURO_ASD_GALLAGHER_REL_2012_07_05 Illumina HiSeq 2000; 72 vcf
EGAD00001000316 UK10K_NEURO_ASD_GALLAGHER REL-2012-11-27 Illumina HiSeq 2000; 75 vcf
EGAD00001000266 This Study uses a focused bespoke bait pull down library method to target findings of Osteosarcoma whole genome and whole exome sequencing studies in order to validate findings. This method will also be used on a larger set of tumour only samples in order to find precedence of these findings in a larger set of patient samples. Illumina HiSeq 2000; 110 bam
EGAD00001000203 Otosclerosis gene discovery Illumina HiSeq 2000; 10 bam
EGAD00001000367 Genomic libraries (500 bps) will be generated from total genomic DNA derived from lung cancer patients and subjected to short paired end sequencing on the llumina platform. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions. Illumina HiSeq 2000; 5 bam
EGAD00001000389 Cancer is driven by mutations in the genome. We will uncover the mutations that give rise to Ewing's sarcoma, a bone tumour that largely affects children. We will use second generation Illumina massively parallel sequencing, and bespoke software, to characterise the genomes and transcriptomes of Ewing's sarcoma tumours. Illumina HiSeq 2000; 20 bam
EGAD00001000384 In order to progress human induced pluripotent stem cells (hiPSCs) towards the clinic, several outstanding questions must be addressed. It is possible to reprogram different somatic cell types into hiPSCs but it is unlcear whether some cell types carry through fewer mutations through reprogramming (either due to mutations present in the primary cells, or mutations accumulated during reprogramming). Through in depth analysis of hiPSCs generated from different somatic cells, it will be possible to assess the variation in genetic stability of different cell types. Illumina HiSeq 2000; 35 bam
EGAD00001000369 We propose to definitively characterise the somatic genetics of a number of pediatric malignant tumours including ependymoma, high grade glioma and central nervous system primitive neurectodermal tumours through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing. Illumina HiSeq 2000; 3 bam