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Sample GSM1574125 Query DataSets for GSM1574125
Status Public on Aug 26, 2015
Title HFF_PD30_Rotenone1
Sample type SRA
 
Source name total RNA extracted from HFF fibroblasts
Organism Homo sapiens
Characteristics population doublings: 30
cell line: HFF
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 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 SAMN03273661
SRA SRX825273

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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