|
| Status |
Public on Feb 01, 2016 |
| Title |
ATAC-seq - mES - 12hr KD, Control ASO rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic Stem Cells_control_antisense_oligonucleotides
|
| Organism |
Mus musculus |
| Characteristics |
cell type: ES cells
cell line: v6.5
gender: male
|
| Treatment protocol |
Cells were depleted of 7SK by nucleofecting antisense oligonucleotides for 12 hours and chromatin state was assayed by transposase
|
| Growth protocol |
mES cells were grown on gelatin plates with serum and LIF.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Transposed DNA was isolated using MinElute Spin columns (Qiagen)
Paired-end libraries were generated as previously described (PMID: 24097267)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
DNA from open and chromatinized DNA
processed data file: mm9_ATAC-seq_12hrControlASO.bw
|
| Data processing |
Library strategy: ATAC-seq
After demultiplexing, reads were stripped adaptors, mapped to the mouse genome (mm9) and processed as previously described (PMID: 24097267)
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files of merged biological replicates of ATAC-seq experiments
|
| |
|
| Submission date |
May 21, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Ryan Alexander Flynn |
| E-mail(s) |
raflynn@stanford.edu
|
| Organization name |
Stanford University
|
| Street address |
380 Roth Way, Room 265
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE69139 |
7SK-BAF axis controls pervasive transcription at enhancers [ATAC-Seq] |
| GSE69143 |
7SK-BAF axis controls pervasive transcription at enhancers |
|
| Relations |
| BioSample |
SAMN03704226 |
| SRA |
SRX1036423 |
