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Sample GSM2872496 Query DataSets for GSM2872496
Status Public on Jun 13, 2018
Title ATAC-seq_Ssrp1-KD_rep2
Sample type SRA
 
Source name mESCs
Organism Mus musculus
Characteristics cell line: E14 cell line
treatment: Ssrp1-KD
Extracted molecule genomic DNA
Extraction protocol Biological replicates were obtained from two independent transfection experiments for each shRNA vector. ATAC-seq was performed on 50,000 cells as previously described (Buenrostro et al, 2013). All samples were PCR amplified for 9 cycles were paired-end sequenced on an Illumina Hi-Seq 2500 platform.
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Data processing Sequenced paired mates were mapped on mm10 genome build using Bowtie2 with the following parameters: –X 2000. Reads corresponding to nucleosome free regions were selected via the “ATACseqQC” R package. All the ATAC-seq BAM files were converted to bigwig, binned (1 bp), and normalised to x1 sequencing depth using Deeptools (v 2.4). Duplicated reads were removed. Chromatin accessibility profiles were visualised using R (v 3.3.0).
Genome_build: mm10
 
Submission date Dec 01, 2017
Last update date May 15, 2019
Contact name Peter Tessarz
E-mail(s) ptessarz@age.mpg.de
Organization name Max Planck Institute
Street address Joseph-Stelzman-Str 9b
City Cologne
State/province Nordrhein-Westfalen
ZIP/Postal code 50931
Country Germany
 
Platform ID GPL17021
Series (1)
GSE90906 Transcriptional repression by FACT is linked to regulation of chromatin accessibility at the promoter of ES cells
Relations
BioSample SAMN08120286
SRA SRX3437618

Supplementary file Size Download File type/resource
GSM2872496_ATAC_Ssrp1KD_rep2.bw 447.7 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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