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| Status |
Public on Aug 26, 2022 |
| Title |
HK2, HIF1, Hypoxia |
| Sample type |
SRA |
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| Source name |
Kidney
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Kidney
cell line: Human Kidney-2
cell type: immortalized
treatment: 1% hypoxia 24 hours
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| Treatment protocol |
1% hypoxia
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| Growth protocol |
DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using an ultrasonicator.
ChIP-seq libraries were prepared using the Truseq v5 Library Preparation Kit. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified on the thermocycler. Post amplification libraries were size selected at 250-450bp in length. Libraries were validated using the Agilent High Sensitivity DNA Kit.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg19 genome. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v1.3.7.1 with the significance cut-off q-value <=0.01
Assembly: UCSCv37,hg19
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| Submission date |
Aug 19, 2022 |
| Last update date |
Aug 28, 2022 |
| Contact name |
Imari Mimura |
| E-mail(s) |
imimura@m.u-tokyo.ac.jp
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| Phone |
81-3-3815-5411
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| Organization name |
The University of Tokyo
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| Department |
Div. Nephrol and Endocrinol.
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| Street address |
7-3-1 Hongo Bunkyo-ku
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| City |
Tokyo |
| ZIP/Postal code |
113-8655 |
| Country |
Japan |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE211665 |
Genome-wide binding sites of Hypoxia inducible factor 1(HI1) in renal epithelial cells. |
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| Relations |
| BioSample |
SAMN30415363 |
| SRA |
SRX17153414 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6482264_cd24_hif1a.bar.gz |
73.6 Mb |
(ftp)(http) |
BAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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