Using Tier 1 expression data, 84% of our lines were classified as pluripotent by PluriTest9 (score > 20) and 97% had a pluripotency score of >10, which yields almost identical sensitivity and specificity in the PluriTest training set (Fig. 1b). Most lines with a pluripotency score <20 (69%) had been cultured on feeder free Essential 8 media (OR 5.4, P < 8x10-13, Fisher’s exact test), which likely reflects that PluriTest was primarily trained using lines grown in feeder-dependent conditions (Extended Data Fig. 2). Using the Cellomics imaging data we quantified the fraction of cells expressing each pluripotency marker individually and estimated that, on average, between 18% and 62% of cells in the iPSC lines co-expressed all three markers NANOG, POU5F1 (OCT4) and SOX2 (Fig. 1c). Almost all lines (>99%) successfully produced cells from all three germ layers during directed differentiation with the average line producing up to 70%, 84% and 77% of cells expressing all three markers of dEN, dME and dEC, respectively (Fig. 1d). We assessed correlations of differentiation capacity between different germ layers and found a positive correlation
