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Sample GSM4798167 Query DataSets for GSM4798167
Status Public on Aug 31, 2021
Title 18/5 WT GFP HIGH 1
Sample type SRA
Source name mEpiLC
Organism Mus musculus
Characteristics cell type: mEpiLC
genotype: WT
fraction: high
Treatment protocol GFP high or low fraction were collected by FACS moflo.
Growth protocol Mouse ES cells were cultured in 2iL. EpiLC differentiation were performed in actinvin a, bFgf and 1% KSR medium.
Extracted molecule genomic DNA
Extraction protocol 50,000 cells were collected and washed with ice-cold PBS once then lysed in the buffer (10 mM Tris-HCl, pH _x000B_7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL). The nuclear pellets were collected and Tn5 tagmentation were performed with Illumina Nextera kit. (FC-121-1030)
Library construction were performed with Illumina Nextera kit. (FC-121-1030)
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2000
Data processing Reads were quality-trimmed using TrimGalore!; reads shorter than 15 nt were discarded.
Reads were aligned to the mouse reference genome (mm10) using bowtie with parameters "-m1 -v1 --best --strata -X 2000 --trim3 1". Duplicates were removed using Picard tools.
Reads shorter than one nucleosome length were discarded, and an offset of 4 nts was introduced.
bigWig tracks were created using deepTools bamCoverage with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig tracks
Submission date Sep 22, 2020
Last update date Aug 31, 2021
Contact name Irina Mohorianu
Organization name University of Cambridge
Department Wellcome-MRC Cambridge Stem Cell Institute
Street address Puddicombe Way
City Cambridge
ZIP/Postal code CB2 0AW
Country United Kingdom
Platform ID GPL13112
Series (2)
GSE158344 ­De novo DNA methylation suppresses aberrant fate trajectory during epiblast transition [ATAC-seq]
GSE158347 Disabling de novo DNA methylation in embryonic stem cells allows an illegitimate fate trajectory
BioSample SAMN16237736
SRA SRX9172064

Supplementary file Size Download File type/resource 152.0 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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