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Status |
Public on Jul 01, 2013 |
Title |
Rapa_S6 |
Sample type |
SRA |
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Source name |
Adult mouse heart, rapamycin diet
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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)
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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.
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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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.
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Submission date |
Jun 17, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Serban Ciotlos |
E-mail(s) |
smelov@buckinstitute.org
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Phone |
4085068553
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Organization name |
Buck Institute for Research on Aging
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Lab |
Melov Lab
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Street address |
8001 Redwood Blvd
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City |
Novato |
State/province |
CA |
ZIP/Postal code |
94945 |
Country |
USA |
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Platform ID |
GPL13112 |
Series (1) |
GSE48043 |
Late life rapamycin treatment reverses age-related heart dysfunction |
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Relations |
BioSample |
SAMN02205754 |
SRA |
SRX308199 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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