Extended Data Fig. 3: Transcriptomic and immunostaining analysis of hSeO.
From: Human assembloid model of the ascending neural sensory pathway
a. Cell type composition in hSeO colored by cluster (left), and UMAP plots of hSeO colored by the hiPS cell line (right). b. UMAP plots of hSeO samples showing selected cell type markers and receptors. c. RT-qPCR of POU4F1 (hCO, n = 7; hDiO, n = 6; hdSpO, n = 8; hSeO, n = 7 samples, from 3 hiPS cell lines from 2–4 differentiation experiments, one-way ANOVA, F3, 24 = 16.59 with Tukey’s multiple comparisons test, ***P = 0.0001, ****P < 0.0001) and SIX1 (hCO, n = 7; hDiO, n = 6; hdSpO, n = 8; hSeO, n = 7 samples, from 3 hiPS cell lines from 2–4 differentiation experiments, one-way ANOVA, F3, 24 = 15.49 with Tukey’s multiple comparisons test, ****P < 0.0001) expression across four regions at day 45–100. d. Immunostaining of VGLUT2 and NeuN in hSeO (left) and quantification of VGLUT2+/NeuN+ co-localization (right) at days 121–125 (n = 6 organoids from 3 hiPS cell lines from 4 differentiation experiments). e. Dot plot showing selected marker gene expression in each cluster. f. Dot plot showing gene expression of several receptors for sensory stimuli. g. Integrated UMAP visualization of scRNA-seq of human primary DRG (PCW 15) and hSeO (human primary DRG, n = 49,705 cells from 7 DRG samples, one individual; hSeO, day 68–72, n = 18,382 cells from 4 hiPS cell lines, same dataset as in Fig. 1 with optimized QC criteria). h. UMAP plot colored by sample identity. i. Dot plot showing selected marker gene expression in each cluster. j. Cell composition of hSeO and human primary DRG based on scRNA-seq. k. UMAP plots showing selected cell type markers and receptors. Data shown as mean ± s.e.m. Dots indicate qPCR samples or organoids in c, d. Each shape represents a hiPS cell line: Circle, 1205-4; Triangle, 1208-2; Diamond, 0410-1; Square, KOLF2.1 J in c, d.
