title: Bulk RNA-Seq of DM1-039
design: RNA was extracted from biopsies via a TRIzol-chloroform extraction supplemented with a bead-based tissue homogenization (Benchmark Scientific) and purified using the Zymo Clean and Concentrator – 5 kit following the standard protocol for on-column DNase treatment. RNA quality and abundance was assessed using fragment analysis (Agilent Fragment Analyzer 5200, DNF-472 (15 nt RNA kit) and Qubit 4 Fluorometer (Invitrogen). Most RNA samples had RIN values >7, but samples were sequenced if they had RIN scores > 5.5. Low quality reads and adapters were trimmed using Trim Galore! and aligned to hg38 reference genome using STAR v 2.7.2d using parameters --twopassMode Basic and sjdbGTffile with a GTF from ensembl release 98. Gene level counts for all samples were obtained wit hfeaturecounts v2.0.0. Differential splicing analysis was performed using rMATS v4.1.0 in paired mode, specifying variable read length. Differential gene expression was quantified using edgeR. Assembly: hg38