Fig. 4
From: Guiding T lymphopoiesis from pluripotent stem cells by defined transcription factors
Single-cell transcriptomic characterization of iHECs and iHPCs. a Principal component analysis (PCA) of iHECs and developmental E11 AGM-derived ECs, T1 pre-HSCs, T2 pre-HSCs, E12 HSCs, E14 HSCs, and adult HSCs. TPM values of genes in iHECs (n = 70), natural E11 AGM-derived ECs (n = 17), T1 pre-HSCs (n = 28), T2 pre-HSCs (n = 32), E12 HSCs (n = 21), E14 HSCs (n = 32) and adult HSCs (n = 47) from single-cell RNA-Seq data were calculated with Stringtie package. b The expression of the top 100 genes contributing most to PC2 (50 genes for each direction). The expression value (TPM) of each gene was converted by log2 and illustrated by pheatmap (R package). One column represents one cell repeat. c Violin plots show the expression profile of selected artery (A)- and vein (V)-related genes (A: Nrp1, Efnb2, and Hey1; V: Nrp2, Nr2f2, and Ephb4) in single iHECs. The expression value (TPM) of each gene was converted by log2 and illustrated by ggplot2 (R package). One point represents one cell. d Violin plots show the expression profile of selected surface markers (Cdh5, Esam, Tek, Procr, Cd47, and Cd63) in single iHECs. The expression value (TPM) of each gene was converted by log2 and illustrated by ggplot2 (R package). One point represents one cell. e Violin plots show the expression profile of selected transcription factors (Fli1, Erg1, Lmo2, Lyl1, Tal1, Sox7, Runx1, Mycn, Gata2, Bcl11a, Hoxa9, and Hoxb5) related to hematopoietic development in single iHECs. The expression value (TPM) of each gene was converted by log2 and illustrated by ggplot2 (R package). One point represents one cell. f Two-dimensional t-SNE analysis of iHEC and iHPC single-cell RNA-Seq. For single-cell RNA-Seq, the iHECs were collected at day 11, and the iHPCs were collected at day 14, 17 and 21. Each dot represents one cell. The TPM values of genes in iHECs (n = 65), iHPCs at day 14 (n = 21), day 17 (n = 18) and day 21 (n = 56) from single-cell RNA-Seq data were calculated with Stringtie package. Cell types were defined as: (1) iHEC, CD31+CD41lowCD45−c-kit+CD201high; (2) day-14 and day-17 iHPC, CD45+Lin(Ter119/Gr1/F4-80/CD2/CD3/CD4/CD8/CD19/FcεRIα)−; (3) day-21 iHPC, Ter119−CD45+c-kit+CD127+. g t-SNE analysis of the expression pattern of selected endothelia-related transcription factors (Sox7, Sox18, and Ets1) in iHECs and iHPCs. h t-SNE analysis of the expression pattern of selected hematopoiesis-related transcription factors (Lyl1, Etv6, Prdm5, Myb, Sfpi1, and Meis1) in iHECs and iHPCs. i t-SNE analysis of the expression pattern of selected T cell development-related transcription factors (Lmo2, Bcl11a, Ikzf1, Myc, Gata3, and Tcf7) in iHECs and iHPCs at day 14, day 17, and day 21. j t-SNE analysis of the expression pattern of selected lymphopoiesis-related surface protein-coding genes (Kit, Flt3, Cd7, Ccr9, Ccr7, and Cxcr4) in iHECs and iHPCs at day 14, day 17, and day 21
