Transcriptional profiles of skeletal muscles in mice exposed to acute hypoxia

To understand the underlying gene changes in in vivo muscles during acute hypoxic exposure, we studied the transcriptional profiles of in vivo skeletal muscles from mice exposed to 8% O2 for 0 hours, 2 hours, and 6 hours. For each condition, we extracted total RNA from fresh in vivo plantaris muscles for 3 biological replicates. The NGS data was acquired using paired-end 100bp by Illumina HiSeq 2000 with a depth around 100X. The quality control of raw data indicated excellent quality of sequencing data with quality scores in the range of 33-40 all over the reads. The analysis of differential expressed genes indicated quick genes responses in skeletal muscles in both 2 and 6 hours of hypoxia. The gene changes indicated a shift from genes associated with extracellular lumen in 2 hours of hypoxia to genes associated with the nuclear lumen in 6 hours of hypoxia. Signaling pathways such as PI3K/Akt signaling, mTOR signaling, MAPK signaling showed enriched gene responses. The KEGG-pathway based pathway-network analysis suggested the PI3K/Akt signaling pathway as a nodal pathway among the gene response-enriched pathways during acute hypoxia. Our Western blot experiments indicated a functional down-regulation of PI3K/Akt signaling by de-phosphorylation of Akt. Overall design: Gene expressions in in vivo skeletal muscles exposed to 8% O2 for 2 hours and 6 hours