|
| Status |
Public on May 21, 2021 |
| Title |
ATAC-Seq 3hr rep1 |
| Sample type |
SRA |
| |
|
| Source name |
human fibroblast + mouse ESC fusion
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
cell type: heterokaryon
treatment: no dnAP-1 (control)
|
| Treatment protocol |
To induce dnAP-1 in fibroblasts, doxycycline was added at the beginning of the co-culture step at 1000 ng/ml
|
| Growth protocol |
Fibroblasts are grown in 10% FBS + DMEM. ESCs are grown with 10% FBS, 10% KSR, LIF, beta-mercaptoethanol in KO DMEM
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were pelleted and permeabilized in hypotonic buffer with 0.1% IGEPAL CA-630. Nuclei were treated with transposase from Illumina (Cat FC-121-1030)
Fragments were amplified with NEBNext PCR master mix and Nextera indices for 8-12 cycles
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
3hr rep1
|
| Data processing |
Default Illumina base calling implementation
Reads were trimmed, and then mapped to concatenated human and mouse genome using Bowtie 2
reads mapping to chrM and those with MAPQ <10 were removed
peaks were called with MACS 2
Genome_build: hg38/mm10
Supplementary_files_format_and_content: bigwig read pileup centered at Tn5 29bp footprint
|
| |
|
| Submission date |
May 05, 2021 |
| Last update date |
May 21, 2021 |
| Contact name |
Helen M Blau |
| Organization name |
Stanford University
|
| Department |
Baxter Laboratories
|
| Street address |
269 Campus Dr
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL25526 |
| Series (2) |
| GSE120992 |
AP-1 is a temporally regulated dual gatekeeper of reprogramming to pluripotency (ATAC-Seq) |
| GSE121053 |
AP-1 is a temporally regulated dual gatekeeper of reprogramming to pluripotency |
|
| Relations |
| BioSample |
SAMN19024203 |
| SRA |
SRX10785147 |
