Processing order was re-randomized prior to ribosomal RNA (rRNA) depletion, and samples were processed in batches of 8. To expedite sequencing, processing began before extraction was complete and randomization occurred among all available extracted samples in sets of 120 to 226. Briefly, rRNA was depleted from about 1 ug of total RNA using Ribo-Zero Magnetic Gold kit (Illumina/Epicenter Cat # MRZG12324) to enrich for polyadenylated coding RNA and non-coding RNA. The Pitt case/control pairs were batched together in each processing step, including Ribo-Zero depletion, sequence library preparation, and sequencing lane. 10 of the Pitt controls were extracted and sequenced as independent duplicates, once as part of a SCZ pair and once as part of a bipolar pair. The sequencing library was prepared using the TruSeq RNA Sample Preparation Kit v2 (RS-122–2001-48 reactions) in batches of 24 samples. The insert size and DNA concentration of the sequencing library was determined on Agilent Bioanalyzer and Qubit, respectively. A pool of 10 barcoded libraries were layered on a random selection of two of the eight lanes of the Illumina flow cell bridge amplified
