Extended Data Fig. 6: Supporting information for in vitro erythroid differentiation experiments.

(a) Reference embedding of bone marrow mononuclear cell CITE-seq reference dataset (left) with gene module scores for selected pathways annotated on the UMAP embedding. (b) Flow cytometry gating scheme used for sorting of in vitro differentiated healthy control and PS cells, related to Fig. 7. (c) Flow cytometry plots showing the distribution of CD71 and CD235a surface marker expression of in vitro differentiated healthy control and PS cells at indicated days of culture. (d) MayGrunwald Giemsa stained cytospins of in vitro differentiated healthy control and PS cells at day 8 of culture at 63x magnification. (e) UMAP of scRNA-seq data colored by predicted cell cycle state. Cluster annotations as in Fig. 7e–g. (f) Comparison of differential gene expression between PT3 donor cells with MDS (x-axis) and without MDS (y-axis) related to healthy control. The Pearson correlation between all genes is annotated (0.82). Genes from relevant pathways or genomic annotations are highlighted in specific colors. (g-i) Projection of gene expression of selected differentially expressed genes between PS and healthy control erythroblasts, including (g) PHGDH, (h) CPOX, and (i) HEBP2. Gene expression coloring is scaled for all plots between the first and 99th quantile per gene.