Gene Expression and Epigenetic Analyses of Human Myocytes from Different Muscles

The study contains expression, DNA methylation data and genomic data of in vitro cultured primary myoblasts, immortalized control myoblast, and mutant myoblasts. The primary myoblasts were derived from biopsies of control, facioscapulohumeral dystrophy 1 (FSHD1) and FSHD2 patients from the tibialis anterior, quadricep, bicep and deltoid. FSHD is linked to DUX4 (Gene ID: 100288687) mRNA expression from the last copy of the D4Z4 repeats on chromosome 4q. The control myoblast cell line was derived from a quadricep biopsy of a healthy individual. The mutant cells, carrying either D4Z4 mutations, SMCHD1 (Gene ID: 23347) mutation or both, were generated from the control myoblast cells by CRISPR-mediated genome editing. Expression data is from bulk RNA-seq using the SmartSeq2 protocol for days 0 and 5 of differentiation of the primary myocytes from the bicep and deltoid of FSHD1 patients, and for days 0, 3/4/5 (early myotubes) and 12/13/14 (late myotubes) of differentiation of the immortalized control and mutant myocytes. DNA methylation data was produced using the TruSeq Methyl Capture EPIC kit (Illumina) for days 0, 3 and 12 of in vitro differentiation of primary myocytes from the tibialis anterior and quadricep of healthy individuals and FSHD2 patients. Genomic data for myoblasts was acquired by targeted, amplification-free DNA sequencing using CRISPR/Cas and the Nanopore sequencing platform. For Electrical Pulse Stimulation (EPS), immortalized control and FSHD patient myocytes were subjected to EPS on day 10 of differentiation using a C-Pace EM culture pacer. Cells with or without EPS stimulation were harvested 6 hours after completion of stimulation for RNA extraction. ]]>
Patient-derived myoblasts were included based on (1) the quality of myoblasts (>70% desmin-positive) with efficient proliferation and differentiation capability, (2) clear diagnosis and clinical phenotype, and (3) their age-matched controls of the same sex (if available). However, since available samples are extremely limited, age and sex may not always match.]]>