NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1941487 Query DataSets for GSM1941487
Status Public on Jan 26, 2016
Title Control ATAC-seq replicate 3
Sample type SRA
 
Source name Control ATAC-seq, ESC
Organism Mus musculus
Characteristics strain: 46C (129/Ola strain)
cell line: ESC line 46C
transfection: control shRNA vector, 48h timepoint, replicate 1
Treatment protocol described in the SAMPLES section (experimental conditions)
Growth protocol Embryonic stem cells were cultured at 37°C, 5% CO2, on mitomycin C-inactivated mouse embryonic fibroblasts, in DMEM (Sigma) with 15% foetal bovine serum and leukemia inhibitory factor (LIF).
Extracted molecule genomic DNA
Extraction protocol 50,000 cells were collected, washed with cold PBS and resuspended in 50ul of ES buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2). Permeabilized cells were resuspended in 50 ul Transposase reaction (1X Tagmentation buffer, 1.0-1.5 ul Tn5 transposase enzyme (Illumina)) and incubated for 30min at 37°C. Subsequent steps of the protocol were performed as described in PMID: 24097267.
Transposed DNA was subjected to several round of amplification with Ad2 primer pairs (the reverse primer contains the index allowing subsequent multiplexing. Oligonucleotide sequences are available in PMID: 24097267). Libraries were next purified using a Qiagen MinElute kit and Ampure XP magnetic beads (1:1.6 ratio) to remove remaining non ligated adapters.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Description library strategy: ATAC-seq
Data processing Basecalling was performed with RTA 1.18.64. Bcl conversions into Fastq and demultiplexing were performed using bcl2fastq version 1.8.3, Sequenced reads were trimmed for adaptor sequence and masked for low-complexity/low-quality sequence with Trimmomatic 0.32, then mapped to mm9 whole genome using bowtie v0.12.7 with parameters -a -m1 --best --strata -v2 p3
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using WigMaker 3 with default parameters; Scores represent the maximum number of reads overlapping in a 25 bp bin
Supplementary_files_format_and_content: BIGWIG files were generated with UCSC tools (v4) using WigToBigWig program
 
Submission date Nov 16, 2015
Last update date May 15, 2019
Contact name Matthieu GERARD
E-mail(s) matthieu.gerard@cea.fr
Organization name CEA
Department I2BC
Lab Mammalian Epigenomics
Street address SBIGeM bldg 142
City Gif-sur-Yvette
ZIP/Postal code 91191
Country France
 
Platform ID GPL17021
Series (1)
GSE64825 Genome-wide distribution and function of ATP-dependent chromatin remodelers in embryonic stem cells
Relations
BioSample SAMN04271244
SRA SRX1433597

Supplementary file Size Download File type/resource
GSM1941487_ATAC-seq_control_transfection_48h_timepoint_replicate_1_B00H5QP_shuf33M.bw 339.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap