The identification of differentially expressed genes in skeletal muscle of wild-type and ob/ob mice

Systemic metabolic homeostasis in mammals is regulated by metabolic organ including skeletal muscle. The mechanisms regulating metabolism in skeletal muscle and how these mechanisms are altered in obesity have yet to be identified. Here we measured transcriptomic data in skeletal muscle of wild-type (WT) and leptin-deficient obese (ob/ob) mice, and identified genes that significantly different in ob/ob mice compared to WT mice as differentially expressed genes. We used ten-week-old male C57BL/6J wild-type and ob/ob mice after overnight (16 hours) fasting. Mice were sacrificed by cervical dislocation and skeletal muscle was dissected and immediately frozen in liquid nitrogen. The frozen tissue was pulverized with dry ice to a fine powder with a blender and separated into tubes. Total RNA was extracted from skeletal muscle using RNeasy Mini Kit (QIAGEN) and QIAshredder (QIAGEN) and assessed for quantity using Nanodrop (Thermo Fisher Scientific) and for quality using the 2100 Bioanalyzer (Agilent Technologies). cDNA libraries were prepared using SureSelect strand-specific RNA library preparation kit (Agilent Technologies). The resulting cDNAs were subjected to 100-bp paired-end sequencing on an Illumina HiSeq2500 Platform (Illumina).