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Sample GSM3417801 Query DataSets for GSM3417801
Status Public on Oct 06, 2018
Title HKC8_3_6hr_HIF2a_rep1
Sample type SRA
 
Source name kidney proximal tubule cell line
Organism Homo sapiens
Characteristics cell line: HKC8
tissue: kidney proximal tubule cell line
degree of hypoxia: 3.0%
duration of hypoxia: 6 hours
chip antibody: HIF2a (PM9)
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 SAMN10180541
SRA SRX4802322

Supplementary file Size Download File type/resource
GSM3417801_6h_3__PM9_1_Treat_nodup_norm.bigwig 134.5 Mb (ftp)(http) BIGWIG
GSM3417801_6h_3__PM9_1_peaks.bed.gz 8.2 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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