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Sample GSM789715 Query DataSets for GSM789715
Status Public on Sep 03, 2011
Title Active_Mstn_deficient_2
Sample type SRA
Source name triceps brachii muscle
Organism Mus musculus
Characteristics activity level: active
tissue: triceps brachii
myostatin genotype: Mstn exon 3 floxed
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
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
Reanalyzed by GSE80797
SRA SRX096383
BioSample SAMN00716164

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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