RNA-seq data of DLPFC release 1.2 was downloaded from the “normalized SVA-corrected” directory of the CMC Knowledge Portal (www.synapse.org/#!Synapse:syn5609499) using Synapse Python client (http://docs.synapse.org/python/). The data being used in this study contained 307 SCZ cases and 245 controls where the paired-end RNA-seq data had been generated on an Illumina HiSeq 2500. Brain tissues in this dataset were obtained from several brain bank collections, including the Mount Sinai National Institutes of Health (NIH) Brain and Tissue Repository, the University of Pittsburgh NeuroBioBank and Brain and Tissue repositories, the University of Pennsylvania Alzheimer’s Disease Core Center, and the National Institute of Mental Health (NIMH) Human Brain Collection Core. Detailed procedure of tissue collection, sample preparation, data generation, and processing can be found in the CMC Knowledge Portal Wiki page (www.synapse.org/#!Synapse:syn2759792/wiki/69613).

The normalized RNA-seq read counts from 143 SCZ cases and 112 controls extracted from cultured primary neuronal cells derived from neuroepithelium were generated as previously described (24). Similar to the CMC data, the raw CNON data consisted of 100–base pair (bp) paired-end reads. The data had been preprocessed to exclude ribosomal RNA (rRNA) and mitochondrial genes. Later, normalized counts were calculated by the DESeq2 software.

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