|
Status |
Public on Aug 31, 2021 |
Title |
1/6 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)
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|
|
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
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|
|
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 |
SAMN16237729 |
SRA |
SRX9172072 |