RNA-seq muscle

Identify the genes modulated by Glucocorticoid Receptor. Overall design: We selectively knocked-out GR in myofibers by crossing GR floxed mice to HSA-Cre-ERT2 mice. RNA from gastrocnemius muscle of 16 week-old control (GR floxed mice) and knock-out mice was extracted with trizol according to the manufacturer protocol. RNA samples were sequenced by the standard Illumina protocol to create raw sequence files (.fastq files). We annotated these reads to the mm10 build of the mouse genome using TopHat version 2. The aligned reads were counted with the homer software (analyze RNA) and DEG's were identified using EdgeR and DESeq.