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Sample GSM1492879 Query DataSets for GSM1492879
Status Public on Nov 06, 2014
Title MRC_5_PD32_3
Sample type SRA
 
Source name total RNA extracted from MRC-5 fibroblasts
Organism Homo sapiens
Characteristics population doublings: 32
cell type: MRC-5 fibroblasts
treatment: control
Treatment protocol MRC-5 fibroblastswere subjected to quiescence using 150 days contact inhibition
Extracted molecule total RNA
Extraction protocol 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.
For library preparation an amount of 2 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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Illumina Casava software used for extraction of FASTQ files
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 (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.p6
Supplementary_files_format_and_content: Excel file including raw counts and RPKM values for each sample
 
Submission date Aug 28, 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)
GSE60883 RNA-seq of young and quiescent MRC-5 human fibroblasts
Relations
Reanalyzed by GSM1553084
Alternative to GSM3336712
BioSample SAMN03012546
SRA SRX689252

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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