|
| Status |
Public on Aug 18, 2016 |
| Title |
p53 IR replicate 3 |
| 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
|
| |
|
| 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 |
SAMN05464349 |
| SRA |
SRX1989077 |
