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Sample GSM1166237 Query DataSets for GSM1166237
Status Public on Jul 01, 2013
Title Rapa_S6
Sample type SRA
 
Source name Adult mouse heart, rapamycin diet
Organism Mus musculus
Characteristics strain/background: C57BL/6
tissue: heart
developmental stage: adult
age: 27 months old
treatment: 14 ppm Rapamycin diet (3 month treatment)
Treatment protocol 24-month-old C57BL/6 mice were fed a diet containing 14 ppm Rapamycin or a control diet for 3 months at which point the heart was removed and frozen at -80C.
Extracted molecule total RNA
Extraction protocol Whole frozen heart tissue was crushed to a powder in liquid nitrogen. The powdered tissue was then treated with Qiasol lysis buffer and extracted for total RNA on a Qiacube robot using the RNeasy mini kit (Invitrogen). The extracted RNA was quantitated using a NanoDrop and RNA quality was measured via BioAnalyzer chip (Agilent).
Oligo-dT purification of polyadenylated RNA, and reverse transcription to create cDNA. The cDNA is fragmented, blunt-ended, and ligated to indexed (barcoded) adaptors. The library is size selected (in the case of paired-end RNA-Seq), size distribution validated using capillary electrophoresis, and quantified using fluorimetry (PicoGreen) and via Q-PCR.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing RNA-Seq (50 bp paired-end sequencing) was carried out on a HiSeq 2000 according to the manufacturer's protocols (Illumina).
Average Quality scores for the completed run across all 20 samples was >30, with an average of 10 million reads per sample.
The completed sequencing reads were then input into CLCBio Genomics Workbench 5 (ClCBio, Cambridge, MA), and mapped to the MGSCv37 C57BL/6J mouse genome (maximum paired distance=300 and minimum=130, minimum number of reads per mapping = 5, maximum number of mismatches= 2, with the reads being mapped to unique sites in the genome).
Using these parameters, 34,293 genes were mapped and used in subsequent differential expression analysis in Bioconductor.
To identify significantly differentially expressed genes in total heart RNA for the comparisons between the rapamycin-treated group (N=10) versus untreated controls (N=10), we used the freely available edgeR package in Bioconductor.
To allow for the comparatively large group size comparisons, a prior of n=1/18 was set in edgeR. We then used an FDR of 5% to detect significantly differentially expressed genes between the two groups that resulted in a list of 700 genes.
Genome_build: MGSCv37
Supplementary_files_format_and_content: 'DE_genes_processed.txt': Tab-separated value file containing the counts per million reads for each individual sample across the 700 differentially expressed genes.
Supplementary_files_format_and_content: 'All_genes.txt': Tab-separated value file containing all of the genes mapped from each sample and counts per million.
 
Submission date Jun 17, 2013
Last update date May 15, 2019
Contact name Serban Ciotlos
E-mail(s) smelov@buckinstitute.org
Phone 4085068553
Organization name Buck Institute for Research on Aging
Lab Melov Lab
Street address 8001 Redwood Blvd
City Novato
State/province CA
ZIP/Postal code 94945
Country USA
 
Platform ID GPL13112
Series (1)
GSE48043 Late life rapamycin treatment reverses age-related heart dysfunction
Relations
BioSample SAMN02205754
SRA SRX308199

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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