Functional dissection of metabolic trait-associated variants in steady state and stimulated human skeletal muscle cells [RNA-Seq]

Type 2 diabetes (T2D) is a common metabolic disorder characterized by dysregulation of glucose metabolism. Genome-wide association studies have defined hundreds of signals associated with T2D and related metabolic traits, most of which are found in noncoding regions. Given their central role in insulin production and glucose homeostasis, much focus has been devoted to investigating T2D-associated genetic variation in pancreatic islets; however, metabolic disease pathogenesis and risk is distributed across other important metabolic tissues, including the liver, adipose, and skeletal muscle. Here, we performed RNA-seq in human skeletal muscle cells in one of four conditions: (1) undifferentiated or differentiated with (2) basal media, (3) media supplemented with the AMP analog 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) to mimic physiological effects of exercise or (4) media containing sodium palmitate which is known to induce insulin resistance. We used these profiles to identify how relevant metabolic stimuli influence transcriptome-wide gene regulation. We collected 15 million LHCN-M2 cells after exposure to one of four conditions: undifferentiated, differentiated, differentiated with 2 mM AICAR or differentiated with 0.5 mM palmitate. We later isolated mRNA-enriched sequencing libraries. We performed paired-end sequencing on an Illumina NovaSeq X instrument.