Extended Data Figure 7: Molecular features of HE-7TF cells.
From: Haematopoietic stem and progenitor cells from human pluripotent stem cells
a, Correlation matrix of RNA-seq data from HSPC populations (CD34+CD38−CD45+) from HE-7TF cells or cord blood HSC engrafted for 12 weeks, iPS-haemogenic endothelium, and publicly available gene expression data (PubMed identifiers 26541609 and 26502406). RNA-seq samples from this study were RSips_7F_Average, RS_HE_Average, and RS_HSC_CB. Samples from ref. 23 were BCP_Average, CLP_Average, Thy_Average, HSC_Average, LMPP_Average, and HSC_CB_Average. The remaining samples are from ref. 24. b, Gene set enrichment analysis signature of HE-7TF cells compared with haemogenic endothelium cells. HE-7TF cells show gene expression signatures that positively correlate with LMO2 targets, TEF1 targets, HOXA4 targets, chemokine receptors and chemokines, TCF4 targets, integrin signal, GATA3 targets, and HSPCs. P < 0.05 and FDR q value < 0.25 were considered significant conditions. All gene set enrichment analysis plots satisfied these conditions, except the HSPC signatures, which had a q value of 0.121 and a P value of 0.06, suggesting that transcriptional differences remain between HE-7TF and bona fide HSCs/HSPCs. HSPC signature taken from ref. 56. c, RPKM values of seven transcription factors and HOXA target genes in indicated cell types are shown. HOXA target genes from ref. 28. PubMed identifier 27183470. d, Heatmap depiction of relative expression levels of the 26 transcription factors in the library in the following samples: HE, HE-7TF cells (engrafted), cord blood HSCs (engrafted), and fresh HSCs and progenitors. Notably, HE-7TF cells show high expression of HOXA family genes, GATA2, TGIF2, SOX4, and EVI1. e, The t-SNE of in-droplet single-cell RNA-seq of HE-7TF cells and cord blood HSCs (engrafted CD34+CD38−CD45+ cells from bone marrow at 12 weeks). The t-SNE from the top 500 most variable genes is presented in the top panel. f, Expression value of 8 haematopoietic genes in the same plot. Notably, the middle population (a subpopulation of HE-7TF cells) shared similar expression values, and degrees of heterogeneity of RUNX1, MEIS1, CD34, TAL1 with cord blood HSCs.
