|
| Status |
Public on Mar 04, 2022 |
| Title |
1h_Hpx_Control_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
HeLa
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: Control siRNA, 1 h 1% oxygen (hypoxia)
cell line: HeLa
|
| Treatment protocol |
Hypoxia treatments were performed by incubating cells in an InvivO2 300 Hypoxia Workstation (Baker Ruskinn) at 1% O2, 5% CO2 and 37 °C. Lysis of hypoxia treated samples was carried inside the hypoxia workstation to avoid reoxygenation. Reoxygenation treatments were performed by incubating cells for 24h in hypoxia followed by 1h incubation at 21% O2, 5% CO2 and 37°C. Cells were transfected with 27 nM of small interfering RNA (siRNA) oligonucleotides (Eurofins) for 48h using Interferin (Polyplus) transfection reagent according to manufacturer’s instructions.
|
| Growth protocol |
HeLa cells were maintained in DMEM supplemented with 10% v/v FBS, 2 mM L-glutamine, 50 units/mL penicillin and 50 μg/mL streptomycin at 5% CO2 and 37 °C. Cells were cultured for no more than 30 passages and routinely tested for mycoplasma contamination using MycoAlert Mycoplasma Detection Kit .
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Omni-ATAC protocol (Corces 2017)
Standard ATAC-seq library construction
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads in fastq files were trimmed for adaptors using Cutadapt and low quality score using Sickle. Reads were aligned to the human genome version hg38 (UCSC) using Bowtie2, sorted and indexed binary alignment mapped (bam) files with mitochondrial reads removed were generated using Samtools.
Bam files were filtered to keep ‘only properly paired reads’ following ENCODE guidelines using Samtools. PCR duplicates were removed from bam files using Picard.
Library sized normalised (reads per kb per million reads (RPKM)) bigwig files were made using deepTools.
Open chromatin regions were identified using MACS2 (--nomodel --shift -100 --extsize 200 -q 0.01) and filtered to remove ENCODE DAC hg38 blacklisted regions and regions with an FDR < 1x10-15.
Genome_build: hg38
Supplementary_files_format_and_content: bed files = peak data, chr start end. bigwig files = library sized normalised alignment data
|
| |
|
| Submission date |
Oct 21, 2021 |
| Last update date |
Mar 04, 2022 |
| Contact name |
Sonia Rocha |
| E-mail(s) |
sonia.rocha@liverpool.ac.uk
|
| Organization name |
University of Liverool
|
| Street address |
Crown Street
|
| City |
Liverpool |
| ZIP/Postal code |
L69 7ZB |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE186342 |
Regulation of Chromatin Accessibility by hypoxia and HIF_1 |
|
| Relations |
| BioSample |
SAMN22486714 |
| SRA |
SRX12727830 |
