Extended Data Fig. 7: Isogenic differentiation and reprogramming system confirms transient-naive-treatment reprogramming corrects transcriptional profiles of hiPSCs.
From: Transient naive reprogramming corrects hiPS cells functionally and epigenetically
a) MA plots showing differentially expressed genes between hESCs and each class of hiPSC (Primed, TNT, NtP). Red points represent significantly differentially expressed genes (log2FC > 1, FDR < 0.05, log2CPM > 1). Plots indicate that TNT-hiPSCs and NtP-hiPSCs are more transcriptionally similar to hESCs than Primed-hiPSCs. b) Barplots (left) show the number of CG-DMRs that intersect promoters, for CG-DMRs detected in hiPSCs compared to hESCs. Colours indicate the proportion of genes linked to promoters that show significant differential expression (FDR < 0.05, log2FC > 1). Scatter plots show the relationship between promoter DNA methylation differences between hiPSCs and hESCs (x-axis) and gene expression differences (y-axis). Individual points indicate DMR-gene pairs, with point colours indicating if the gene was differentially expressed. c) Heatmap showing clustered standardised gene expression values for differentially expressed genes with fibroblast-associated gene ontology terms. d) Gene expression levels for early mesoderm lineage genes. Grey points represent individual samples, n = 2 independent experiments per group, error bars show mean and range. e) Gene expression heatmap of fibroblast-specific genes with retained expression in Primed-hiPSCs.
