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Sample GSM892957 Query DataSets for GSM892957
Status Public on Jun 12, 2012
Title Wild type
Sample type SRA
Source name WT_ESCs
Organism Mus musculus
Characteristics strain: Cast/Eij /129/Sv
genotype/variation: wild type
cell type: Embryonic stem cell (ESC)
Treatment protocol For ChIP-seq the cells were treated for 3 h with proteasome inhibitor (15uM, MG132, Sigma) before chromatin was cross-linked for 10 min at RT with 1% formaldehyde. The cross-linking reaction was stopped by addition of 0.125 M glycine.
Growth protocol Female ESCs expressing V5-tagged REX1 and control wild-type ESCs were grown without feeders to 80% confluence (3·107 cells per ChIP or 1·108 cells per ChIP-seq).
Extracted molecule genomic DNA
Extraction protocol Purified ChIP-DNA was prepared for sequencing on a HiSeq 2000 sequencer using Illumina standerd protocol.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Data processing Basecalling , Illumina pipeline 1.7.0
Read Alignment, Eland, Illumina pipeline 1.7.0
import, filter, normalize and coverage calculation, using R based bioconductor packages (Shortread and ChIP-Seq packages)
peak calling using using R based bioconductor package(MACS)
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph
Submission date Mar 10, 2012
Last update date May 15, 2019
Contact name Eskeatnaf Mulugeta Achame
Phone 0031614883537
Organization name Erasmusmc
Department Reproduction and Development
Lab Reproduction and Development
Street address Dr Molewaterplein 50
City Rotterdam
State/province Rotterdam
ZIP/Postal code 3015 GE
Country Netherlands
Platform ID GPL13112
Series (1)
GSE36417 ChIP-sequencing (ChIP-seq) experiments on female ESCs expressing V5-tagged REX1 and control wild-type Embryonic stem cells (ESCs)
SRA SRX128353
BioSample SAMN00810990

Supplementary file Size Download File type/resource
GSM892957_ctrl_all.cov.bedGraph.gz 280.7 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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