Comment[ArrayExpressAccession] E-GEOD-54333 MAGE-TAB Version 1.1 Public Release Date 2014-04-25 Investigation Title EDD: a program for detection of wide genomic enrichment domains robust against local variations [RNA-Seq] Comment[Submitted Name] EDD: a program for detection of wide genomic enrichment domains robust against local variations [RNA-Seq] Experiment Description Nuclear lamins contact the genome at the nuclear periphery through large domains and are involved in chromatin organization. Among broad peak calling algorithms available to date, none are suited for mapping lamin-genome interactions genome-wide. We disclose a novel algorithm, Enriched Domain Detector (EDD), for analysis of broad enrichment domains from ChIP-seq data. EDD enables discovery of genomic domains interacting with broadly distributed chromatin-associated proteins such as lamins. The main advantage of EDD over existing broad peak callers is sensitivity to domain width rather than enrichment strength at a particular site, and robustness against local variations. EDD is downloadable from http://github.com/eivindgl/edd. RNA-seq experiments in human normal dermal fibroblasts (Lonza CC-2511; LDFs) and human normal primary dermal fibroblasts (Norwegian Stem Cell Center AD04DFs). Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name Collas Collas Lund Oldenburg Person First Name Philippe Philippe Eivind Anja Person Email geo@ncbi.nlm.nih.gov Person Affiliation University of Oslo Person Address Institute of Basic Medical Sciences, University of Oslo, PO Box 1112 Blindern, Oslo, Norway Person Roles submitter Protocol Name P-GSE54333-4 P-GSE54333-1 P-GSE54333-3 P-GSE54333-2 Protocol Description reads aligned with tophat v2.0.8b with parameter M-bM-^@M-^Sno-novel-juncs transcript abundance estimated with cufflinks v2.1.1 with parameter M-bM-^@M-^SGTF csv file created from column 5 and 10 from cufflinks output file genes.fpkm_tracking Genome_build: hg19 Supplementary_files_format_and_content: csv with two columns; gene_short_name and fpkm value Cells were cultured as described under Growth protocol. 2x10e6 cells were cultured to confluency for RNA preparation before harvesting to ensure consistency of cell cycle stages between the two cell types. Total RNA was isolated using the Ambion TRIzolM-. Reagent RNA extraction kit (Life Technologies), quality checked using a BioAnalyzer 2100 and processed for library preparation. RNAseq library was prepared according to the Illumina protocol, and sequenced on an Illumina HiSeq2500 at the Norwegian Sequencing Center. Human normal dermal fibroblasts (Lonza CC-2511; LDFs) and human normal primary dermal fibroblasts (Norwegian Stem Cell Center AD04DFs) were cultured in DMEM/F12 containing 13% FCS, 2 ng/ml basic fibroblast growth factor and antibiotics. Cells were exponentially growing and used at passage 5-7. AD04DFs were obtained with Norwegian Ethics Committee Approval REK2617A. Protocol Type normalization data transformation protocol sample treatment protocol nucleic acid library construction protocol growth protocol Experimental Factor Name CELL LINE CELL TYPE Experimental Factor Type cell line cell type Publication Title Enriched domain detector: a program for detection of wide genomic enrichment domains robust against local variations. Publication Author List Lund E, Oldenburg AR, Collas P PubMed ID 24782521 Publication DOI 10.1093/nar/gku324 Comment[SecondaryAccession] GSE54333 Comment[GEOReleaseDate] 2014-04-25 Comment[ArrayExpressSubmissionDate] 2014-01-23 Comment[GEOLastUpdateDate] 2014-05-07 Comment[AEExperimentType] RNA-seq of coding RNA Comment[SecondaryAccession] SRP035617 Comment[SequenceDataURI] http://www.ebi.ac.uk/ena/data/view/SRR1141005-SRR1141006 SDRF File E-GEOD-54333.sdrf.txt