Bulk RNA-Seq, chimpanzee (Pan troglodytes) iPSC-derived neurons
Total RNA was extracted from cells (1-2 wells, 6 well plate) using an RNeasy Plus Mini Kit (Qiagen), including a DNase step to remove residual DNA. Total RNA was analyzed for quality using the Agilent Bioanalyzer system (Agilent RNA 6000 Nano kit) with RNA Integrity Numbers (RINs) for all samples between 8.3-10 (SI Table 1). Using the NEBNext Poly(A) Magnetic mRNA Isolation Kit (NEB), mRNA was isolated from intact total RNA, and cDNA libraries were made from each sample using the NEBNext RNA Ultra II Library Prep Kit for Illumina (New England Biolabs). Barcoded samples were sequenced using the Illumina NextSeq 500 platform at the Genomics Resource Core Facility (Institute for Applied Life Sciences, UMass Amherst) to produce 75 base pair single-end reads, yielding a minimum of 32 million reads per sample.