The Chinese University of Hong Kong (CUHK) Circulating Nucleic Acids Research Group (CNARG)

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jiangpeiyong@cuhk.edu.hk

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This DAC controls 29 datasets

Dataset ID	Description	Technology	Samples
EGAD00001000284	Cancer Genome Scanning in Plasma: Detection of Tumor-Associated Copy Number Aberrations, Single-Nucleotide Variants, and Tumoral Heterogeneity by Massively Parallel Sequencing	Illumina Genome Analyzer IIx	1
EGAD00001000290	Cancer Genome Scanning in Plasma: Detection of Tumor-Associated Copy Number Aberrations, Single-Nucleotide Variants, and Tumoral Heterogeneity by Massively Parallel Sequencing	Illumina Genome Analyzer IIx	1
EGAD00001000308	Cancer Genome Scanning in Plasma: Detection of Tumor-Associated Copy Number Aberrations, Single-Nucleotide Variants, and Tumoral Heterogeneity by Massively Parallel Sequencing		1
EGAD00001000395	Noninvasive Prenatal Molecular Karyotyping from Maternal Plasma		1
EGAD00001000856	None	Illumina HiSeq 2000	1
EGAD00001001093	Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing	Illumina HiSeq 2000	2
EGAD00001001275	None	Illumina HiSeq 2000	1
EGAD00001001602	None	Illumina HiSeq 2000	1
EGAD00001001609	Maternal Plasma RNA Sequencing for Genomewide Transcriptomic Profiling and Identification of Pregnancy-Associated Transcripts		14
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 NextSeq 500	32
EGAD00001003778	None	Illumina HiSeq 2000	1
EGAD00001004204	We used targeted sequencing to capture and measure the abundance as well as the size profiles of EBV DNA in plasma of subjects with and without NPC	Illumina HiSeq 2500 NextSeq 500	337
EGAD00001004291	We performed ATAC-seq experiments using 2 placental samples and 2 buffycoat samples.	Illumina HiSeq 2500	4
EGAD00001004324	This dataset consist on 70 maternal plasma samples (bam files) used in the FetalQuantSD. The maternal plasma DNA samples were sequenced using the HiSeq 2000 platform (Illumina) with a 50-cycle paired-end mode.	Illumina HiSeq 2000	70
EGAD00001004561	Plasma DNA libraries were constructed from 4 mL of plasma without library enrichment, namely without PCR amplification. Paired-end massively parallel sequencing was performed	Illumina HiSeq 2000	169
EGAD00001004568	We performed whole genome bisulfite sequencing of plasma DNA in 11 colorectal cancer patients to study the colonic DNA in plasma.	Illumina HiSeq 2500	17
EGAD00001004590	DNA-seq from plasma of 14 liver transplantation patients	Illumina HiSeq 4000	14
EGAD00001005071	We showed that mice in which Dnase1l3 had been deleted showed aberrations in the fragmentation of plasma DNA. We also observed a change in the ranked frequencies of end motifs of plasma DNA caused by the Dnase1l3 deletion.	NextSeq 500	41
EGAD00001005088	None	NextSeq 500	236
EGAD00001005093	None	Illumina HiSeq 4000	118
EGAD00001005286	We developed a new bioinformatics method for detecting the eccDNA in plasma. We revealed that the biological properties between eccDNA and linear DNA are different. eccDNA could be potentially provided as a new class of circulating biomarker.	Illumina HiSeq 1500 Illumina HiSeq 2500	15
EGAD00001005371	The biology of cell-free DNA fragmentation and the roles of DNASE1, DNASE1L3 and DFFB	NextSeq 500	40
EGAD00001006054	Data were generated by next-generation sequencing (Illumina) in a fastq format. This dataset involved sequencing data from pregnant women and patients with hepatocellular carcinoma (HCC). For HCC samples, the paired buffy coat and tumor DNA tissue samples were also sequenced.	Illumina HiSeq 4000	29
EGAD00001006215	Human dnase1l3 deficiency-Mouse AAV samples	NextSeq 500	5
EGAD00001006216	Plasma DNA profile in DNASE1L3 deficiency	NextSeq 500 Sequel	37
EGAD00001006875	In this study, we enhanced 5mC detection using SMRT sequencing by holistically analyzing kinetic signals of a DNA polymerase and sequence context for every base within a measurement window. We employed a convolutional neural network to train a methylation classification model.	NextSeq 500 Sequel II	42
EGAD00001007041	We developed Genetic-Epigenetic Tissue Mapping (GETMap) to determine the tissue composition of plasma DNA carrying genetic variants not present in the constitutional genome through comparing their methylation profiles with relevant tissues.	Illumina HiSeq 4000 NextSeq 500	152
EGAD00001007750	The dataset contains 2x75bp paired-end sequencing data in DNASE1L3-deficient human subjects. We performed bisulfite sequencing of plasma samples from three DNASE1L3-deficient subjects and one heterozygous parent to investigate how nuclease deficiencies alter plasma cell-free DNA methylation profiles.	Illumina HiSeq 1500 Illumina HiSeq 4000	7
EGAD00001007751	The dataset contains sequencing data in wildtype, Dnase1-deficient and Dnase1l3-deficient mice. We performed 2 x 75bp paired-end whole genome bisulfite sequencing of pooled plasma cell-free DNA (cfDNA) and buffy coat genomic DNA. The effects of DNASE1L3 or DNASE1 deficiency on cfDNA methylation was explored in plasma of mice deficient in these nucleases.	Illumina HiSeq 4000 NextSeq 500	36