|
| Status |
Public on Oct 06, 2018 |
| Title |
RCC4_Normoxia_INPUT repeat 2 |
| Sample type |
SRA |
| |
|
| Source name |
kidney cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: RCC4
tissue: kidney cancer cell line
degree of hypoxia: normoxia
duration of hypoxia: --
chip antibody: input chromatin
|
| Treatment protocol |
Hypoxic incubations were performed for the specified duration and ambient oxygen concentration in an In Vivo2 400 Hypoxia Work Station (Ruskinn Technology).
|
| Growth protocol |
Cell lines were grown in Dulbecco’s modified Eagle’s Medium, 100 U/ml penicillin, 100 μg/ml streptomycin and 10% fetal bovine serum (Sigma Aldrich) and regularly tested for mycoplasma infection.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitation (ChIP) experiments were performed using antibodies directed against HIF-1a (rabbit polyclonal, PM14), HIF-2a (rabbit polyclonal, PM9), or HIF-1b (rabbit polyclonal, Novus Biologicals, NB100-110).
Libraries were prepared from immunoprecipitated chromatin using the Illumina ChIP-Seq kit
All ChIP-seq experiments were performed in duplicate in accordance with ENCODE consortium guidelines
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Illumina adaptor sequences were trimmed using Trimgalore (0.3.3) and reads were aligned to Genome Reference Consortium GRCh37 (hg19) using BWA (0.7.5a-r405). Low quality mapping was removed (MapQ < 15) using SAMtools (0.1.19)
Low quality mapping was removed (MapQ < 15) using SAMtools (0.1.19) and reads mapping to Duke Encode black list regions (http://hgwdev.cse.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeMapability) were excluded using BEDTools (2.17.0)
Duplicate reads were marked for exclusion using Picard tools (1.106) (http://picard.sourceforge.net/).
ChIP-seq peaks were identified using T-PIC (Tree shape Peak Identification for ChIP-Seq) and MACS (Model-based analysis of ChIP-Seq) in control mode
Peaks detected by both peak callers were filtered quantitatively using the total count under the peak to include only peaks that were above the 99.99th percentile of random background regions selected from the ENCODE DNASE II cluster (p-value < 0.0001).
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: bigwig and bed files of called peaks
|
| |
|
| Submission date |
Oct 05, 2018 |
| Last update date |
Oct 08, 2018 |
| Contact name |
David Robert Mole |
| E-mail(s) |
david.mole@ndm.ox.ac.uk
|
| Phone |
0044 (0)1865 613956
|
| Organization name |
University of Oxford
|
| Department |
Nuffield Department of Medicine
|
| Lab |
NDM Research Building
|
| Street address |
Roosevelt Drive, Headington
|
| City |
Oxford |
| ZIP/Postal code |
OX3 7FZ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE120885 |
Inherent DNA binding specificities of the HIF-1α and HIF-2α transcription factors in chromatin (ChIP-seq) |
| GSE120887 |
Inherent DNA binding specificities of the HIF-1α and HIF-2α transcription factors in chromatin |
|
| Relations |
| BioSample |
SAMN10181177 |
| SRA |
SRX4802355 |
