GSE119761
Comparison Between Sost-CreERT2 and wild type Cre- Gastrocnemius Skeletal Muscle Transcriptomes
Purpose: The purpose of this study is to identify the age when the skeletal muscle phenotype in Sost-CreERT2 mice occurs. Methods: Gastrocnemius skeletal muscle mRNA profiles of 1-month-old Sost-CreERT2 and wild type Cre- male mice and 3-month-old Sost-CreERT2 and wild type Cre- female mice were generated by deep sequencing, in triplicate, using HiSeq4000. The sequencing data were first assessed using FastQC (Babraham Bioinformatics, Cambridge, UK) for quality control. Then all sequenced libraries were mapped to the mm10 mouse genome using STAR RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”. The reads distribution across the genome was assessed using bamutils (from ngsutils). Uniquely mapped sequencing reads were assigned to mm10 refSeq genes using featureCounts (from subread) with the following parameters: “-s 2 -p –Q 10”. Quality control of sequencing and mapping results was summarized using MultiQC. Genes with read count per million (CPM) > 0.5 in more than 2 of the samples were kept. The data was normalized using TMM (trimmed mean of M values) method. Differential expression analysis was performed using edgeR. False discovery rate (FDR) was computed from p-values using the Benjamini-Hochberg procedure. Results: In the male mice there were 1,857 2fold upregulated genes and 1,959 2fold downregulated genes, whereas in females there were 37 upregulated and 34 downregulated genes.  Only 14 upregulated and 21 downregulated genes overlapped between males and females. A pathway analysis of the male gastrocnemius was performed showing that inflammation mediated by chemokine and cytokine signaling pathways was the major upregulated pathway in Sost-CreERT2 as compared to wild type Cre– male mice.  The Wnt signaling pathway was the major downregulated pathway in the Sost-CreERT2 male mice. Overall design: Gastrocnemius skeletal muscle mRNA profiles of 1-month-old Sost-CreERT2 and wild type Cre- male mice  and 3-month-old Sost-CreERT2 and wild type Cre- female mice were generated by deep sequencing, in triplicate, using HiSeq4000.