|
| Status |
Public on Jan 12, 2016 |
| Title |
Senes_Treated_Replicate_2 |
| Sample type |
SRA |
| |
|
| Source name |
Senes_Treated
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Parkin-expressing MRC5 fibroblasts
cell state: Mitochondrial deficient senescent
treatment: CCCP
|
| Treatment protocol |
Parkin-expressing MRC5 fibroblasts were irradiated with 20Gy X-ray and 2 days after were treated with 12.5uM CCCP for 48h (refreshed every 24 hours). At day 4 after irradiation, CCCP was removed and cells were kept in culture with normal serum supplemented medium. Cells were harvested at day 10 after irradiation (6 days after CCCP treatment) for RNA-seq analysis.
|
| Growth protocol |
MRC5 human fibroblasts were grown in Dulbecco’s Modified Eagle’s Medium (DMEM, Sigma, Dorset, UK) supplemented with 10% heat inactivated foetal calf serum (FCS), 100 units/ml penicillin, 100 μgml-1 streptomycin, 2mM glutamine and 50 μgml-1 uridine at 37oC in a humidified atmosphere incubator with 5% CO2
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using Qiagen RNeasy mini kit according to the manufacturer instructions with on the column DNASE I digestion.
Quality of RNA was assessed on Agilent 2100 Bioanalyzer using Agilent RNA 6000 Nano Kit (Agilen Technologis), before creating oligo-dT based cDNA library using Illumina TruSeq RNA Sample Prep Kit,v2.0. kit.
The library was sequenced on a NextSeq500, using a NextSeq500 Mid Output kit 150 cycles flowcell.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were trimmed using Trim Galore (v0.3.0).
Paired-end reads are aligned to the human genome (hg19) using tophat2. Reference splice junctions were provided by a reference transcriptome (Ensembl build 73).
FPKMs were determined using cufflinks under default settings.
Differentially expressed genes were called using cuffdiff under default settings.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix of FPKMs for all samples, as called by cufflinks. Differential gene expression for uninduced vs induced samples, as called by cuffdiff.
|
| |
|
| Submission date |
Dec 17, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter Adams |
| Organization name |
University of Glasgow, Beatson Institute for Cancer Research
|
| Street address |
Switchback Rd, Bearsden
|
| City |
Glasgow |
| ZIP/Postal code |
G61 1BD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE76125 |
Effect of mitochondria deficiency on senescence-associated gene expression |
|
| Relations |
| BioSample |
SAMN04349611 |
| SRA |
SRX1490489 |
