|
| Status |
Public on Mar 27, 2014 |
| Title |
HIF1a_Hypoxia_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
Caki-2 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: ccRCC
tissue: kidney
chip-antibody: HIF-1a antibody (Novus, NB100-134)
|
| Treatment protocol |
Cells were treated with 100 μM desferoxamine (DFO) induced hypoxic conditions
|
| Growth protocol |
Caki-2 was maintained in McCoy's 5a modified medium supplemented with 10% (vol/vol) fetal bovine serum
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitation was performed in Caki-2 cells with a HIF-1a antibody (Novus, NB100-134) and control IgG antibody
Libraries were prepared according to Solid's insruction for single-end library.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
AB SOLiD 4 System |
| |
|
| Data processing |
ChIP-seq reads were aligned to the hg18 genome assembly using BWA with default configurations.
The aligned reads were filtered to get uniquely mapped reads.
Peaks were called using MACS1.4 with p value cutoff <= 0.00001.
Genome_build: hg18
Supplementary_files_format_and_content: Chr represents chromosome; start represents the start position of the peak; end represents the end position of the peak; length represents the length of the peak; summit represents the relative position of summit of the peak; tags represent the number of reads in the peak; -10*log10(pvalue) represent the p value of the peak; fold_enrichment represents the fold change of the peak compared with local genome background.
|
| |
|
| Submission date |
Jan 23, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Jing Zhang |
| E-mail(s) |
henry.jingzhang@gmail.com
|
| Organization name |
Columbia University Medical Center
|
| Street address |
1130 St Nicholas Ave ICRC, room403
|
| City |
Beijing |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL13393 |
| Series (1) |
| GSE54327 |
Genome-wide maps of HIF1a binding sites in ccRCC cell line under hypoxia condition |
|
| Relations |
| BioSample |
SAMN02595633 |
| SRA |
SRX447964 |
