(A) Representative bright field (top) and fluorescence (bottom) images of the hESC GFP12 line at passage 2, 10, and 20 after SeV-GFP infection. (B) Expression levels of 63 genes that were identified to be significantly different between 3 biological replicates of hESC GFP and 3 biological replicates of hESC SC lines within each of the two genetic backgrounds (FDR<0.01 and fold change >2 or <0.5; see details in the Methods section). Green and grey boxes indicate the expression ranges for each differentially regulated gene in 6 hESC GFP and 6 hESC SC lines, respectively. TPM; transcripts per million. (C) Heatmap and dendrogram separating all isogenic hESC lines based on the 63 DEGs shown from Fig. 2B. hESC SC lines, dark blue; hESC GFP lines, light blue. (D) Heatmap and dendrogram for all isogenic hESC and hiPSC lines based on pairwise Pearson correlation (r) of global gene expression levels (log-scaled). hiPSC lines, red; hESC lines, blue.