|
| Status |
Public on Mar 11, 2024 |
| Title |
HIF1α-mutant 3h hypoxia rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
MCF7
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: breast adenocarcinoma
cell line: MCF7
genotype/variation: HIF1alpha-mutant
treatment: hypoxia (1% oxygen, 3 hours)
|
| Treatment protocol |
Hypoxia treatments for 3 or 24 hours were performed in a Baker Ruskinn InVivo2 400 hypoxic workstation at 1% O2, 5% CO2, 37°C and 70% humidity.
|
| Growth protocol |
MCF7 cells were were cultured in high-glucose DMEM (Gibco, Cat# 11960-085) supplemented with 10% fetal calf serum (FCS), 2 mM L-glutamine and 100 U/mL penicillin/streptomycin in a humidified incubator at 37°C, 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were washed 3x with PBS and harvested in 1 ml TRIzol Reagent (Thermo Fisher Scientific). Chloroform (0.2 ml, Acros Organics) was added to lysates and after shaking (5s) samples were centrifuged for 18 min at 10,000 x g. The aqueous phase was mixed with an equal volume of 100% ethanol (500 μl) and RNA was purified using the RNeasy Kit (Qiagen), according to the manufacturer's instructions.
Libraries were prepared using the KAPA Hyper Prep kit (Roche) according to the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Transcript reads were aligned to the Ensembl GRCh37 genome using Tophat2 v2.1.1 (with option --no-coverage-search).
Gene expression was normalised using DeSeq2 v1.16.1 with default settings.
Genome_build: Ensembl GRCh37
Supplementary_files_format_and_content: tab delimited, contains normalised read counts
|
| |
|
| Submission date |
Nov 01, 2018 |
| Last update date |
Mar 11, 2024 |
| Contact name |
Dimitrios Anastasiou |
| E-mail(s) |
dimitrios.anastasiou@crick.ac.uk
|
| Organization name |
The Francis Crick Institute
|
| Department |
Cancer Metabolism Laboratory
|
| Street address |
1 Midland Road
|
| City |
London |
| ZIP/Postal code |
NW1 1AT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE122059 |
RNA levels in wild-type and HIF1α-mutant MCF7 cells in normoxia (21% O2), and in hypoxia (1% O2) for 3 h or 24 h |
|
| Relations |
| BioSample |
SAMN10358947 |
| SRA |
SRX4964921 |
