|
Status |
Public on Aug 26, 2015 |
Title |
MRC5_PD42w_2 |
Sample type |
SRA |
|
|
Source name |
total RNA extracted from MRC-5 fibroblasts
|
Organism |
Homo sapiens |
Characteristics |
population doublings: 42 cell line: MRC-5 cell type: fibroblasts treatment: 100 nM rotenone
|
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 2.5 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 2000 |
|
|
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
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|
|
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 |
GPL11154 |
Series (1) |
GSE64553 |
RNA-seq of human fibroblasts during normal aging and during aging with rotenone perturbation |
|
Relations |
BioSample |
SAMN03273622 |
SRA |
SRX825247 |