NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4798178 Query DataSets for GSM4798178
Status Public on Aug 31, 2021
Title 18/5 DKO GFP HIGH 2
Sample type SRA
 
Source name mEpiLC
Organism Mus musculus
Characteristics cell type: mEpiLC
genotype: Dnmt3a3b double KO
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
E-mail(s) data-submissions@stemcells.cam.ac.uk
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
Relations
BioSample SAMN16237726
SRA SRX9172075

Supplementary file Size Download File type/resource
GSM4798178_DKO.GFP_HIGH.cell_1.2.bw 167.4 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