|
| Status |
Public on Sep 03, 2011 |
| Title |
Sed_Quad |
| Sample type |
SRA |
| |
|
| Source name |
skeletal muscle
|
| Organism |
Mus musculus |
| Characteristics |
activity level: sedentary
tissue: quadriceps
|
| Treatment protocol |
At 6 months of age, 7 of 10 mice transferred to individual cages with running wheels for a 12 week period.
|
| Growth protocol |
Until 6 months of age, all mice housed 2-3 per cage with ad lib access to food and water and 12 h dark cycle (6PM-6AM)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted with Trizol reagent and polyadenylated RNA was extracted from 8 total RNA pools (each pool from one muscle group of 3 sedentary or 7 active mice) by binding to oligo-dT. The polyA-RNA was eluted, ligated to adapters, converted to cDNA, amplified, and barcoded with the Applied Biosystems whole transcriptome library preparation kit according to instructions provided with the kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD System 3.0 |
| |
|
| Data processing |
50-base reads were mapped to the mouse genome (mm9) with default settings of Bioscope v1.3 software. Reads mapping to exons of Refseq transcripts were counted with Bioscope v1.3 software. Exon-level data were consolidated to gene-level read counts and summarized for all 8 samples in a single table. Data were normalized so that the trimmed column means (excluding values above 97.5 %ile and below 2.5 %ile) were the same for all samples. The 13 protein-coding mtDNA transcripts were mapped to xxxx and counted separately, then normalized to the trimmed mean of the non-mitochondrial transcripts.
|
| |
|
| Submission date |
Sep 01, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Stephen Welle |
| E-mail(s) |
swelle@rochester.rr.com
|
| Organization name |
University of Rochester
|
| Street address |
601 Elmwood Avenue
|
| City |
Rochester |
| State/province |
NY |
| ZIP/Postal code |
14642 |
| Country |
USA |
| |
|
| Platform ID |
GPL9318 |
| Series (2) |
| GSE31843 |
Effect of wheel running exercise on gene expression in skeletal muscles of mice |
| GSE31844 |
Effects of wheel running exercise and myostatin depletion on skeletal muscle gene expression in mice |
|
| Relations |
| SRA |
SRX096323 |
| BioSample |
SAMN00716099 |
