|
| Status |
Public on Jul 16, 2020 |
| Title |
ESC_p300KD_ATAC-Seq_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: 129/C57Bl/6/ICR
cell type: Embryonic stem cells
genotype/variation: p300 KD
|
| Treatment protocol |
ESCs were infected with lentivirus packaged with p300 and CBP shRNA plasmid (Dharmacon). The day after the lentivirus infection, the media was replaced with complete mESC culture media containing 1 μg/ml puromycin (for p300 plasmid) or 400 ug/ul (for CBP plasmid) of G418. After 4 days of selection, mESCs were used for downstream analysis.
|
| Growth protocol |
ESCs were cultured under standard conditions (KO-DMEM, 2 mM Glutamax, 15% ES grade fetal bovine serum, 0.1 mM 2-mercaptoethanol, and leukemia inhibitory factor (LIF)). For early passages, cells were maintained on an irradiated feeder layer. To remove feeders, cells were passaged at least two passages off of feeders onto gelatin-coated plates.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples were prepared according to the Illumina Nextera protocol.
Libraries were constructed according to the Illumina Nextera protocol.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The ATAC-seq reads were aligned to the mm10 mouse reference genome using the BWA aligner (Li and Durbin, 2010).
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 200-bp windows across the genome using BEDTools for presentation as genome browser tracks (Quinlan et al., 2010).
The sequence length was 33 for R1 and 33 for R2 for paired-end data.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig
|
| |
|
| Submission date |
Oct 15, 2019 |
| Last update date |
Jul 16, 2020 |
| Contact name |
Laura Banaszynski |
| E-mail(s) |
laura.banaszynski@UTSouthwestern.edu
|
| Organization name |
University of Texas Medical Center
|
| Department |
Green Center for Reproductive Biology Sciences
|
| Street address |
5323 Harry Hines Blvd
|
| City |
Dallas |
| State/province |
TEXAS |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE138923 |
Differential contribution of p300 and CBP to regulatory elements in mESCs [ATAC-seq] |
| GSE138925 |
Differential contribution of p300 and CBP to regulatory elements in mESCs |
|
| Relations |
| BioSample |
SAMN13037208 |
| SRA |
SRX7001438 |
