|
Status |
Public on Oct 06, 2018 |
Title |
HKC8Hypoxia0.1O2rep2 |
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: 0.5% duration of hypoxia: 16 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 |
|
|
Description |
sample split over two lanes
|
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 |
SAMN10181211 |
SRA |
SRX4802369 |