|
| Status |
Public on Sep 29, 2023 |
| Title |
P3_5_input |
| Sample type |
SRA |
| |
|
| Source name |
MOUSE FIBROBLAST
|
| Organism |
Mus musculus |
| Characteristics |
chip-grade antibody: none
2nd antibody: none
treatment: 12h 1 mM DMOG treatment
|
| Treatment protocol |
After growing to 60% confluency, cells were changed fresh culture medium with 1mM DMOG. After 12h, cells were harvested.
|
| Growth protocol |
MAF was cultured under 5% CO2,20% O2,37 ℃ with DMEM (10% FBS, 1% PS)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Unsynchronized and confluent pika/rat Epas1 knock-in MAF cells in 15 cm dishes were treated with 1 mM DMOG for 16 h. After treatment, cells were cross-linked in DMEM containing 1 mM DMOG, PMSF, and 1% formaldehyde for 12 min at room temperature. The cross-link was stopped by adding glycine to a final concentration of 125 mM and incubated at room temperature for 5 min. ChIP assay and DNA sample preparation were performed strictly following the ChIP-IT High Sensitivity Kit instructions (Active Motif). Eluted DNA was analyzed with quantitative PCR and high-throughput sequencing.
Libraries were prepared according to Illumina's instructions
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie version 1.2.2 with parameters -p 30 -m 1 -S -q
peaks were called using MACS2 version 2.2.7.1 with parameters callpeak -g mm -B --SPMR
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were converted from bdg files generated by MACS2 version 2.2.7.1, reprsenting fold enrichment for each sites
|
| |
|
| Submission date |
Sep 29, 2020 |
| Last update date |
Sep 29, 2023 |
| Contact name |
wang jiawen |
| E-mail(s) |
wangjiawen2013@gmail.com
|
| Organization name |
National institute of biological sciences
|
| Street address |
7 Science Park Road ZGC Life Science Park
|
| City |
Beijing |
| ZIP/Postal code |
102206 |
| Country |
China |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE158760 |
ChIP-seq data from pika Epas1 knock in MAF and RNA-seq data from mouse, rat, rabbit and Tibetan pika fibroblasts |
|
| Relations |
| BioSample |
SAMN16293058 |
| SRA |
SRX9215475 |
