Transcriptomic analysis of day 1 (D1) differentiating WT and HDAC11-deficient mouse myoblasts

To get insight into the transcriptomic changes caused by HDAC11 loss at early myogenic differentiation, we performed RNA sequencing (RNA-Seq) in 24 h differentiated primary myoblasts from WT and HDAC11-deficient mice. Satellite cell-derived primary myoblasts were obtained after FACS isolation of skeletal muscle cells by growing them at low confluence in proliferation medium. To induce myoblast differentiation, cells were plated at high confluence and changed to differentiation media. Gene Ontology (GO) analysis of the genes upregulated in HDAC11 KO differentiating myoblasts revealed a statistically significant enrichment of cell cycle-related processes while the downregulated genes in HDAC11 KO differentiating myoblasts were enriched in “muscle system process” and “muscle contraction” GO categories. This is an mRNA sequencing study which addressed the effect of loss of Hdac11 gene on gene expression. A total of six samples were inlcuded in the study: Three biological replicates derived from Hdac11 knock out mice and three derived from wild type mice. The polyA+ RNA fraction was sequenced using Illumina technology and differential expression was assessed by comparing normalized sequencing read count levels between the two conditions.