|
| Status |
Public on Jan 25, 2023 |
| Title |
EB_H33WT_ATAC-Seq_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
EB_H33WT_ATAC-Seq_rep2
|
| Organism |
Mus musculus |
| Characteristics |
strain background: 129/C57Bl/6/ICR
genotype/variation: H33WT
tissue/cell type: Embryoid bodies
|
| 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. EBs were differentiated for four days using the hanging drop method.
|
| 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 seqeunce length was 33 for R1 and 33 for R2 for paired-end data.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig
|
| |
|
| Submission date |
Oct 27, 2021 |
| Last update date |
Jan 25, 2023 |
| Contact name |
Laura Banaszynski |
| E-mail(s) |
[email protected]
|
| Organization name |
UT Southwestern Medical Center
|
| Department |
Green Center for Reproductive Biology Sciences
|
| Street address |
5323 Harry Hines Blvd
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390-8511 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE186684 |
Histone variant H3.3 facilitates open chromatin at promoters [ATAC-seq] |
| GSE186687 |
Histone variant H3.3 facilitates open chromatin at promoters. |
|
| Relations |
| BioSample |
SAMN22601604 |
| SRA |
SRX12798482 |
