Fig. 3

iPSC-derived hematopoietic progenitor cells. a Schematic representation of the protocol used for hematopoietic differentiation of iPSCs. b Representative phase contrast images of produced hematopoietic progenitor cells on day 16 of hematopoietic differentiation. Scale bar = 500 μm. c Absolute count of harvested iHPCs per well. Statistics were calculated with 1-way ANOVA and Tukey’s post hoc test; n = 7 for wildtype (WT), n = 4 for each knockout (*P < 0.05; mean ± SD). d Surface marker expression of hematopoietic progenitors. Statistics were calculated with 2-way ANOVA and Tukey’s post hoc test; n = 7 for WT, n = 4 for each knockout (*P < 0.05; **P < 0.01, ***P < 0.001, ****P < 0.0001; mean ± SD). e Total number of colonies formed in CFU assays. Statistics were calculated with 1-way ANOVA and Tukey’s post hoc test; n = 7 for WT, n = 4 for each knockout (*P < 0.05; mean ± SD). f Scatter plots show β-values for all measured CpG sites (grey) when comparing the mean of wildtype iHPCs, exon 19^−/− iHPCs or exon 23^−/− iHPCs with their respective iPSC counterparts. Hypermethylated CpGs are depicted in red, hypomethylated CpGs in blue with delta mean β-value >0.5 or <−0.5. CpG sites associated with promotor regions are shown without transparency. g A deconvolution algorithm [18] was used to estimate the composition of different mature hematopoietic cell types based on the DNAm profiles of our iHPCs, those of Nishizawa et al. [19] and of our previously published iHPC data [20]. h Gene expression changes compared between WT iHPCs and exon 19^−/− or exon 23^−/− iHPCs depicted as log₂ fold change against the mean of normalized counts of all samples regarding sequencing depth (=base mean). Significantly differentially expressed genes are highlighted