|
| Status |
Public on Oct 06, 2018 |
| Title |
RCC4_VHL_Hx_3_Replacement |
| Sample type |
SRA |
| |
|
| Source name |
kidney cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: RCC4+VHL
tissue: kidney cancer cell line
degree of hypoxia: 1.0%
duration of hypoxia: 24 hours
|
| 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 |
polyA RNA |
| Extraction protocol |
Total RNA was prepared using the mirVana miRNA Isolation Kit (Ambion; Life Technologies Ltd, Paisley, UK) and treated with DNaseI (TURBO DNA‐free, Ambion).
PolyA+ RNA libraries were then prepared using the ScriptSeq v2 RNA‐Seq kit (Epicentre, Madison, WI, USA).
All RNA-seq experiments were performed in triplicate in accordance with ENCODE consortium guidelines
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Illumina adaptor sequences were trimmed using Trimgalore (0.3.3)
Reads were aligned to GRCh37 using Tophat 2.0.8b (http://ccb.jhu.edu/software/tophat/index.shtml) and bowtie 1.0.0 (http://bowtie-bio.sourceforge.net/index.shtml) and non-uniquely mapping fragments excluded using SAMtools (0.1.19)
Total read counts for each UCSC defined gene were extracted using HTSeq (0.5.4p3) with ‘intersection-strict’ mode
Significantly regulated genes were identified using DESeq2
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: tab-delimited text files from htseq
|
| |
|
| 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) |
| GSE120886 |
Inherent DNA binding specificities of the HIF-1α and HIF-2α transcription factors in chromatin (RNA-seq) |
| GSE120887 |
Inherent DNA binding specificities of the HIF-1α and HIF-2α transcription factors in chromatin |
|
| Relations |
| BioSample |
SAMN10181192 |
| SRA |
SRX4802376 |
