|
| Status |
Public on Mar 09, 2018 |
| Title |
SIPS_3 |
| Sample type |
SRA |
| |
|
| Source name |
dermis from human abdominoplasty
|
| Organism |
Homo sapiens |
| Characteristics |
cells type: human dermal fibroblasts
cell line: HDF161
population doubling: 15
|
| Treatment protocol |
Prior to treatment fibroblasts were seeded at 3,500 cells /cm2 and quiescent cells were allowed to reach confluence for the next 11 days with a media change on day 4, 7 and 11, whereas premature senescence was induced by exposing the cells 1 hour per day to growth medium supplemented with 100 µM H2O2 on day 1, 2, 3, 4, 7, 8, 9, 10 and 11. On day 11 after the last H2O2 treatment was conducted, half of the SIPS and quiescent cells were cultivated with growth medium supplemented with 0.01 % of 1201. On day 14 the medium was refreshed. On day 15 cells were harvested.
|
| Growth protocol |
Fibroblasts were cultivated in DMEM/Ham's F12 supplemented with 4 mM L-glutamine and 10 % fetal calf serum at 37 °C, 7% CO2 and ambient oxygen. Cells were usually passaged twice a week at a 1:2 ratio.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with TRIreagent (Sigma) following the recommended protocol. RNA concentration and quality was analysed with a Bioanalyzer 2100 using the RNA 6000 Nano Kit (Agilent Technologies) before the samples were sent for next generation sequencing.
RNA libraries were prepared for sequencing on HiSeq 2500 (Illumina) using standard Illumina protocols by GATC BIOTECH (Konstanz, Germany)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Senescent cells replicate 3
|
| Data processing |
Illumina Casava 1.8.2 software was used for basecalling.
RNA-seq reads were aligned to hg19 genome assembly using TOPHAT Version 2.0.13 with default parameters
Cufflinks Version 2.2.1 was used to calculate Fragments Per Kilobase of transcript per Million mapped reads (FPKM) based on .bam files from TOPHAT results
Genome_build: hg19
Supplementary_files_format_and_content: Output files from cufflinks (.gtf) for each sample include FPKM values as feature abundance measurement
|
| |
|
| Submission date |
Jan 12, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Markus Schosserer |
| E-mail(s) |
markus.schosserer@meduniwien.ac.at
|
| Organization name |
Medical University of Vienna
|
| Department |
Center for Pathobiochemistry and Genetics
|
| Lab |
Markus Schosserer
|
| Street address |
Waehringer Strasse 10
|
| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE93535 |
RNAseq of quiescent (Q) and stress induced premature senescent (SIPS) fibroblasts treated with plant extract (1201) from Solidago vigaurea subspecies alpestris |
|
| Relations |
| BioSample |
SAMN06219889 |
| SRA |
SRX2486130 |
