Each iPSC line was passaged on average 16 times before being expanded for the collection of initial molecular data for quality control (‘Tier 1 assays’). These included genotyping (‘gtarray’), gene expression data (‘gexarray’), and an assessment of the pluripotency and differentiation potential of each line (‘Cellomics’). Pluripotency of the lines was additionally verified in silico, using the PluriTest assay 9. Following Tier 1 assays, one or two lines were selected from a subset of donors (hereafter ‘selected lines’) and further expanded to enable collection of a richer set of molecular data (‘Tier 2 assays’). The criteria for line selection were: (i) level of pluripotency, as determined by the PluriTest assay (ii) number of copy number abnormalities and (iii) ability to differentiate into each of the three germ layers. These included proteomics, DNA methylation (‘mtarray’), RNA-sequencing and high-content cellular imaging. Once Tier 1 genotyping data were collected (see below) cell lines originating from the same donor were checked for possible sample swaps using BCFtools (bcftools gtcheck -G1).
