|
| Status |
Public on Jan 26, 2021 |
| Title |
DMSO_NRF2KO_MED1 |
| Sample type |
SRA |
| |
|
| Source name |
WT 9-12_Nrf2 knockout_vehicle
|
| Organism |
Homo sapiens |
| Characteristics |
cell line background: WT 9-12
cell type: immortalized epithelial cell line obtained from patients with ADPKD
genotype/variation: Nrf2 knockout
treatment: DMSO
chip antibody: Bethyl, A300-793A
|
| Growth protocol |
WT 9-12 cells were cultured in DMEM/F-12 medium supplemented with 10% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were cross-linked with 1% formaldehyde in 1 mL PBS for 10 min at RT. The crosslink was quenched by adding 67 μL of 2.5 M glycine(150 mM final). Cells were washed with PBS and harvested using ChIP lysis buffer. Cells were then sonicated to obtain fragments (200-500 bp) with Sonicator. Immunoprecipitation was performed with indicated antibodies. After elution and reversal cross-linking, DNA was purified for library preparation.
Library construction were performed using VAHTS Universal DNA Library Prep Kit (Vazyme, ND607-02) and VATHS DNA Adapters set2 for Illumina (Vazyme Biotech, Cat.N802-01)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Bowtie2 (version 2.3.4.1) was used to align paired-end 150 bp sequence reads to human (hg38) genome
HOMER (version 4.10) findPeaks command was used to call peak
BamCoverage within deeptools (version 3.3.0) were used to generate bigwig files from bam files.
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig
|
| |
|
| Submission date |
Mar 09, 2020 |
| Last update date |
Jan 29, 2021 |
| Contact name |
Zhiheng Liu |
| E-mail(s) |
[email protected]
|
| Organization name |
Tianjin Medical University
|
| Department |
Tianjin Research Center for Basic Medical Science
|
| Lab |
Gene Expression Laboratory
|
| Street address |
No.22 Qixiangtai Road
|
| City |
Tianjin |
| State/province |
Tianjin |
| ZIP/Postal code |
300070 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (2) |
| GSE141739 |
Nrf2-mediated enhancer activation ameliorates oxidative stress and cystogenesis in autosomal dominant polycystic kidney disease [ChIP-seq] |
| GSE141741 |
Nrf2-mediated enhancer activation ameliorates oxidative stress and cystogenesis in autosomal dominant polycystic kidney disease |
|
| Relations |
| BioSample |
SAMN14341651 |
| SRA |
SRX7884419 |
