|
Status |
Public on Aug 18, 2016 |
Title |
p53 IR replicate 1 |
Sample type |
SRA |
|
|
Source name |
MCF-7 breast cancer cells
|
Organism |
Homo sapiens |
Characteristics |
cell line: MCF-7 genotype: p53_delta treatment: IR
|
Treatment protocol |
Cells were either incubated with 4 uM Nutlin-3 for 8 h, irradiated at 5 Gy and subsequently incubated for 4 h or left untreated.
|
Growth protocol |
Cells were cultured in Dulbecco’s Modified Eagle’s Medium supplemented with 10% fetal bovine serum (Firstlink), Pen-Strep and 2 mM L-Glutamine (Sigma-Aldrich) at 37 oC in 5% CO2
|
Extracted molecule |
total RNA |
Extraction protocol |
Trizol/chloroform-extracted total RNA was further purified with the RNeasy Mini Kit (Qiagen) incorporating a DNaseI step (Qiagen) to remove DNA contamination. Libraries were prepared from rRNA-depleted total RNA isolates and according to standard Illumina guidelines using in-house adapters (Lamble et al., 2013)
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
|
|
Data processing |
Reads were aligned to the human reference genome (GRCh37) using TopHat2 with default parameters except for setting mate-inner-dist=100 and mate-std-dev=50 Duplicate reads were removed using Picard Tools MarkDuplicates Counts for Ensembl-annotated genes were summarised from the mapped reads using ht-seq, and filtered to exclude genes with fewer than 10 reads on average per sample Analysis for differential expression was performed using the edgeR package Genome_build: GRCh37 Supplementary_files_format_and_content: Text files containing raw read counts
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|
|
Submission date |
Jul 29, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Jonathan Ross Chapman |
E-mail(s) |
rchapman@well.ox.ac.uk
|
Organization name |
Wellcome Trust Centre for Human Genetics
|
Department |
Nuffield Department of Medicine (University of Oxford)
|
Street address |
Roosevelt Drive
|
City |
Oxford |
ZIP/Postal code |
OX3 7BN |
Country |
United Kingdom |
|
|
Platform ID |
GPL20301 |
Series (1) |
GSE84986 |
53BP1 integrates DNA repair and p53-dependent cell fate decisions via distinct mechanisms |
|
Relations |
BioSample |
SAMN05464373 |
SRA |
SRX1989053 |