|
| Status |
Public on Aug 31, 2021 |
| Title |
23/5 DKO ES 1 |
| Sample type |
SRA |
| |
|
| Source name |
mES cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mES cells
genotype: Dnmt3a3b double KO
|
| 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 |
SAMN16237741 |
| SRA |
SRX9172066 |
