Fig. 5: SOX17 boundary perturbation leads to endoderm differentiation failure.

a Principal component analysis of RNA-seq data, depicting sample clusters by the use of the 100 most variable genes. The first two principal components (PCs) are displayed. Arrows and numbers indicate group comparisons. GSEA of differentially expressed genes between compared groups are indicated below; significantly enriched biological processes are depicted in black, pathways in gray. b TPM Z-score row normalized clustering of the most variable genes (n = 4,151). c TPM values shown for a subset of genes (n = 3 biological replicates). The box indicates the interquartile range (IQR), the line inside the box shows the median. d Wnt stimulation/antagonization utilizing fluorescence activated cell sorting (FACS) data of wild-type and SOX17^∆5’CTCF iPSC at day 5 definitive endoderm. CXCR4 (CD184) is depicted as percentage CXCR4⁺ in bulk cell populations. The upper panel shows DKK2/3/4 inhibition and controls (treatment for 5 consecutive days) (n = 3 biological replicates). Data are presented as mean values ± SD. The lower panel depicts human recombinant DKK1 treatment and controls (for 5 consecutive days) (n = 2 biological replicates). Data are presented as mean values. e DKK4 Enzyme-linked Immunosorbent Assay (ELISA), a quantitative measure of human DKK4 in cell culture supernatants over time (n = 3 biological replicates (averaged) over 2 experiments). Data are presented as mean values. f qRT-PCR of bulk populations from a subset of genes related to Wnt signaling, mesendoderm, endoderm, and pluripotency over 5 days endoderm differentiation. Expression values are depicted as relative gene-expression (2^{-(ΔCt(GOI-18s))}) (n = 2 biological replicates). Data are presented as mean values.