|
| Status |
Public on May 16, 2020 |
| Title |
pkd1_input |
| Sample type |
SRA |
| |
|
| Source name |
epithelial cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Kidney
cell type: pkd1(PH)
chip antibody: none
|
| Growth protocol |
pkd1 and null cells were cultured in DMEM-F12 medium supplemented with 3% fetal bovine serum (FBS) and 1% penicillin/streptomycin,1% Insulin-Transferrin-Selenium, IFNγ, Nystatin suspension and T3.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
pkd1 and null cells were cross-linked with 1% formaldehyde for 10 min at RT. The crosslink was stopped by adding 1/20 volume of 2.5 M glycine. Cells were washed with PBS and harvested using ChIP lysis buffer. Cells were then sonicated to obtain fragments (100-500 bp) with Bioruptor Sonicator. Immunoprecipitation was performed with H3K27ac antibody (Abcam cat# ab4729). After elution and reversal cross-linking, DNA was purified and sequenced on BGISEQ-500.
Construction of ChIP-seq library was completed by BGI company (Shenzhen,China).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
ChIP-seq data were mapped to mus musculus genome (mm10) by SOAPaligner/SOAP2
ChIP-Seq peaks were generated using peak finding algorithm MACS (Model-based Analysis for ChIP -Seq, version: MACS-1.4.2)
Reads mapped only once at locus were allowed for peak calling.
Genome_build: mm10
Supplementary_files_format_and_content: Wig files were generated by MACS-1.4.2.
|
| |
|
| Submission date |
Dec 02, 2019 |
| Last update date |
May 16, 2020 |
| Contact name |
Zeyun Mi |
| E-mail(s) |
mizeyun@tmu.edu.cn
|
| Phone |
15900207057
|
| Organization name |
Tianjin Medical University
|
| Street address |
Qi Xiang Tai Road
|
| City |
Tianjin |
| ZIP/Postal code |
300070 |
| Country |
China |
| |
|
| Platform ID |
GPL23479 |
| Series (2) |
| GSE141279 |
SE-driven metabolic reprogramming in ADPKD (ChIP-Seq) |
| GSE141281 |
SE-driven metabolic reprogramming in ADPKD |
|
| Relations |
| BioSample |
SAMN13446748 |
| SRA |
SRX7255693 |
