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Sample GSM1842792 Query DataSets for GSM1842792
Status Public on Jun 02, 2016
Title NCCIT.input
Sample type SRA
 
Source name NCCIT cells
Organism Homo sapiens
Characteristics cell line: NCCIT Embryonal Carcinoma cell line
chip antibody: none
Growth protocol mESCs were grown in standard ESC medium containing Lif, 1 μM MEK1/2 inhibitor (PD0325901) and 3 μM GSK3 inhibitor (CHIR99021). NCCIT cells were grown in RPMI1640 with 10% FBS.
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. Fragments of 300±100 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR), using Q5 polymerase (NEB M0530).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Data processing Reads were mapped to mm9 or 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: mm9 and hg19
Supplementary_files_format_and_content: FP10M-normalized bigWigs
 
Submission date Aug 03, 2015
Last update date May 15, 2019
Contact name Danny Reinberg
E-mail(s) reinbd01@nyumc.org
Phone 212-263-9036
Organization name NYU School of Medicine / HHMI
Street address 522 First Avenue, 2nd floor Rm 211
City New York City
State/province New York
ZIP/Postal code 10016
Country USA
 
Platform ID GPL11154
Series (2)
GSE71675 A Co-repressor CBFA2T2 regulates pluripotency and germline development [ChIP-seq]
GSE71676 A Co-repressor CBFA2T2 regulates pluripotency and germline development
Relations
BioSample SAMN03952770
SRA SRX1131598

Supplementary file Size Download File type/resource
GSM1842792_NCCIT.input.bw 80.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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