|
| Status |
Public on Jun 22, 2021 |
| Title |
ATAC-Seq p53KOC9-rep2 |
| Sample type |
SRA |
| |
|
| Source name |
ESCs
|
| Organism |
Mus musculus |
| Characteristics |
agent column: ESC maintained in 2i+LIF
cell type: Embryonic stem cell Rx:GFP KI
genotype: p53 knockout clone C9
|
| Treatment protocol |
2% matrigel added at EB day 1.
|
| Growth protocol |
Rx:GFP mESCs were induced to differentiation with SFEBq method (5%KSR in GMEM media)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
5x104 cells were used for transpoistion at 37C for 30 min using Illumina Nextera DNA Library Prep Kit.
Libraries were prepared with the Illumina Nextera DNA Library prep kit according to the manufacturer’s protocol.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
p53KOC9-rep2
|
| Data processing |
Reads were aligned to the mm10 genome assembly using bowtie2 version 2.3.5
Data were filtered using samtools with the following specifications: alignments with MAPQ smaller than 10 were skipped.
Peaks were called from sample 1 to sample 12 using Genrich version 0.6 with the following parameters: -jyv -e MT.
Peaks were called from sample 13 to sample 16 using MACS2 version 2.1.2 with the following parameters: --nomodel --shift -100 --extsize 200 -B --broad -f BAMPE --keep-dup all.
Signals from different biological replicates were first merged, and then were normalized by calculating the log2 ratios over their mean DESeq2 size factors of all biological replicates.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig and peaks table
|
| |
|
| Submission date |
Jun 21, 2021 |
| Last update date |
Jun 22, 2021 |
| Contact name |
Rajesh C Rao |
| E-mail(s) |
rajeshr@umich.edu
|
| Organization name |
University of Michigan
|
| Street address |
1000 Wall Street
|
| City |
Ann Arbor |
| State/province |
Michigan |
| ZIP/Postal code |
48105 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE178551 |
Chromatin accessibility profiling of mouse embryonic stem cells and embryonic bodies using SFEBq differentiation methods upon Wdr5 and P53 deletion with or without WT or mutant hWDR5 rescue |
| GSE178556 |
Wdr5 |
|
| Relations |
| BioSample |
SAMN19796491 |
| SRA |
SRX11188224 |
