This three-step analysis, with filtering for low-expressed transcripts, was used to compare each SCZ-derived hGPC cell line to the pooled CTR-derived hGPCs. The intersection of the resulting 4 individual lists of differentially expressed genes was taken as the conserved representative list of SCZ-dysregulated genes. In the normalization procedure for each comparison, the number of RUVs-calculated variance factors was limited to 1 for line 29, 3 for lines 8 and 164, and 7 for line 51, as determined by principal component and hierarchical clustering analyses performed with native R functions (https://www.R-project.org). To obtain average fold changes and P values for dysregulated genes in all 4 SCZ hGPC lines, a differential expression comparison of pooled SCZ to pooled CTR lines was performed by the same filtering and analysis workflow with the number of variance factors limited to 9.
