Fig. 5: Cells with ^1q and 20q11.21 gain outcompete wt cells during differentiation, but only RPE^1q correctly specify despite showing transcriptomic signatures of aneuploidy-related stress.

a Images of the entire culture dishes during RPE differentiation of co-cultures of fluorescently labelled hESC with a gain of 1q and their isogenic genetically balanced counterparts (VUB03^{1q21.1qter-BLUE} and VUB03^1q32.1-VENUS). The plots indicate the percentages of 1q cells at the start and end of differentiation, mean and standard deviation, two passages after colony picking, as measured by flow cytometry (n = 3 different differentiation experiments, unpaired t-test). b Immunostaining for ZO-1, PMEL, PAX6, and BEST1 for the 1q cells isolated by flow cytometry (in a) and the RPE cells obtained from VUB03^1q32.21 (in Supplementary Fig. 5). c Principal component analysis and d differential gene expression volcano plot for the bulk RNA sequencing of RPE^wt (N = 10) and RPE^1q (N = 9). e Fold-change induction of genes characteristic of RPE and of the pluripotent state, in RPE^wt and RPE^1q, relative to undifferentiated hESC. f GSEA Hallmark pathways are significantly deregulated in the bulk RNA sequencing of RPE^1q vs RPE^wt. g Images of the culture dishes during RPE differentiation of co-cultures of 1% fluorescently labelled cells with a gain of 20^q11.21 and an iso20q and their isogenic genetically balanced counterparts. h Percentage of GFP or mCherry-positive area over time in differentiation. i Immunostaining for ZO-1 and PMEL of the purified RPE cells, along with GFP and mCherry signal.