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Sample GSM1180131 Query DataSets for GSM1180131
Status Public on Dec 25, 2013
Title MRC5-iPS-25_GFP.JARID2
Sample type SRA
 
Source name MRC-iPS-25
Organism Homo sapiens
Characteristics transgene: GFP
ip antibody: JARID2
antibody source: in-house
antibody lot: PC-11
Treatment protocol cells were transduced with lentiviruses encoding either GFP or the MEG3 lncRNA
Growth protocol Human iPSCs were maintained on irradiated MEFs in 0222 medium (MED SHIROTORI CO., Ltd, Tokyo, Japan) supplemented with 10 ng/ml recombinant human basic fibroblast growth factor
Extracted molecule genomic DNA
Extraction protocol Cells were lysed in ChIP buffer (50 mM Tris-HCl pH 7.9, 150 mM NaCl, 1% Triron X-100, 0.5% NP-40, 5 mM EDTA pH 8.0, 1 mM PMSF and protease inhibitor) and chromatin was sonicated to ~200 bp with a Diagenode Bioruptor
Libraries were prepared according to manufacturer’s instructions (Illumina). Immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), and ligated to custom adapters with LigaFast (Promega, city, state #M8225). Fragments of 300±50 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR), using Phusion DNA polymerase (NEB M0530).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Data processing mapped to hg19 with BOWTIE -m4 -v2
1nt resolution bedgraphs were generated with the BEDtools bamToBed and genomeCoverageBed utilities after extending each read to 200
coverage was normalized to FP10M (fragments per 10 million reads sequenced)
bigWig files were generated with bedGraphToBigWig
Genome_build: hg19
Supplementary_files_format_and_content: FP10M-normalized bigWigs
 
Submission date Jul 03, 2013
Last update date Feb 04, 2022
Contact name Roberto Bonasio
Organization name University of Pennsylvania
Department Cell and Developmental Biology
Lab Bonasio
Street address 3400 Civic Center Blvd - SCTR 9-111
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL11154
Series (2)
GSE48515 ChIP-seq in MRC5 hIPSCs overexpressing MEG3 RNA.
GSE48518 Interactions between JARID2 and noncoding RNAs regulate PRC2 recruitment to chromatin
Relations
BioSample SAMN02225315
SRA SRX317571

Supplementary file Size Download File type/resource
GSM1180131_MRC5-iPS-25_GFP.JARID2.v2m4bhg19ren.bg.bw 246.6 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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