|
| Status |
Public on Sep 03, 2011 |
| Title |
Active_control_3 |
| Sample type |
SRA |
| |
|
| Source name |
triceps brachii muscle
|
| Organism |
Mus musculus |
| Characteristics |
activity level: active
tissue: triceps brachii
myostatin genotype: normal
|
| Treatment protocol |
At 6 months of age, 6 of 12 mice (3 of each genotype) 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). From four to six months of age, regular chow was replaced with chow containing 0.025% (w/w) tamoxifen except for two 1-wk breaks with regular chow, for total of 6 weeks of tamoxifen feeding. Tamoxifen feeding depleted myostatin only in mice with floxed myostatin genes.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted with Trizol reagent as directed by Invitrogen. Polyadenylated RNA was extracted, converted to cDNA, and amplified with an Illumina TruSeq RNA library preparation kit as directed by the vendor.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
65-base reads were mapped to the mouse genome (mm9) with default settings of CASAVA software. Reads mapping to exons of Refseq transcripts were counted with CASAVA software. Exon-level data were consolidated to gene-level read counts and summarized for all 12 samples in a single table. Data were normalized so that the trimmed column means (excluding values above 95th %ile and below 5th %ile) were the same for all samples. The 13 protein-coding mtDNA transcripts were mapped to NC_005089.1 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) |
[email protected]
|
| Organization name |
University of Rochester
|
| Street address |
601 Elmwood Avenue
|
| City |
Rochester |
| State/province |
NY |
| ZIP/Postal code |
14642 |
| Country |
USA |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE31839 |
Effect of wheel running exercise and myostatin depletion on gene expression in triceps brachii muscles of mice |
| GSE31844 |
Effects of wheel running exercise and myostatin depletion on skeletal muscle gene expression in mice |
|
| Relations |
| Reanalyzed by |
GSE80797 |
| SRA |
SRX096381 |
| BioSample |
SAMN00716162 |
