|
| Status |
Public on Aug 26, 2015 |
| Title |
HFF_PD58_woRotenone2 |
| Sample type |
SRA |
| |
|
| Source name |
total RNA extracted from HFF fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
population doublings: 58
cell line: HFF
cell type: fibroblasts
treatment: none
|
| Treatment protocol |
The media were changed and rotenone was supplemented every 3 days, due to the half-life of rotenone [Cabras et al., 2002].
|
| Growth protocol |
The fibroblasts were maintained in the presence of rotenone throughout their span (from young PD till senescent) in culture in dim light, due to the light sensitive nature of rotenone [Dekker et al., 2011].
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For library preparation an amount of around 1 μg of total RNA per sample was processed using Illumina’s TruSeqTM RNA Sample Prep Kit (Illumina; San Diego; CA, USA) following the manufacturer’s instruction.
Total RNA was isolated using QIAzol (Qiagen, Hilden, Germany) based on the phenol/chloroform extraction method. Afterwards the RNA was quantified photometrically with a NanoDrop 1000 (PeqLab, Erlangen, Germany) and stored at -80 °C until use.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
FASTQ files were extracted using Illumina Casava software v1.8.2 (sample 1-24) or bcl2fastq v1.8.4 (sample 25-60)
FASTQ files were mapped using Tophat (v2.0.6) vs. the H.sapiens genome GRCh37.66 obtained from Ensembl
Uniquely mapped reads were counted for each gene_id using featureCounts v1.4.3-p1 (featureCounts -T 8 -a $GTF -s 0 -t exon -g gene_id -o featureCounts_gene.txt $SAMFILE)
RPKM values were computed using exon lengths provided by featureCounts and the sum of all mapped reads per sample
Genome_build: GRCh37.66
Supplementary_files_format_and_content: Excel file including raw counts and RPKM values for each sample
|
| |
|
| Submission date |
Dec 29, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
JenAge Project |
| E-mail(s) |
geo-data@jenage.de
|
| Organization name |
Leibniz Institute for Age Research - Fritz Lipmann Institute
|
| Street address |
Beutenbergstr. 11
|
| City |
Jena |
| ZIP/Postal code |
D-07745 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE64553 |
RNA-seq of human fibroblasts during normal aging and during aging with rotenone perturbation |
|
| Relations |
| BioSample |
SAMN03273651 |
| SRA |
SRX825289 |
