Extended Data Fig. 10: Analysis of Forebrain (FB) cluster and Spinal cord (SC)-related cells in µNTLS.
From: A patterned human neural tube model using microfluidic gradients
a. D-V patterning of FB, leading to formation of dorsal pallium and ventral subpallium domains. Pallium is marked by PAX6 and EMX2 expression, whereas subpallium is marked by NKX2-1. b. UMAP plots of FB clusters in CS15-16 human embryo data (left) and day 21 µNTLS data (right). FB cluster in day 21 µNTLS data is annotated following human reference data42 (see Methods). c. Stacked bar plots showing percentages of cells for each FB subcluster in CS15-16 human FB cluster and day 21 µNTLS FB cluster. d. Dot plot showing expression of key marker genes across different cell subclusters in day 21 µNTLS FB cluster and CS15-16 human embryo FB cluster as indicated. Dot sizes and colors indicate proportions of cells expressing corresponding genes and their averaged scaled values of log-transformed expression, respectively. e. Heatmap showing relative expression (Z-score) of top-30 gene signatures calculated from CS15-16 human FB cells in both CS15-16 human FB cluster and day 21 µNTLS FB cluster as indicated. For gene signature information, see Supplementary Table 1. f. Enrichment of Gene Ontology (GO) terms in DEGs upregulated in day 21 µNTLS FB cells or CS15-16 human FB cells as indicated. For detailed information about DEGs and GO terms, see Supplementary Table 1. g. In vivo, dorsal SC gives rise to roof plate (RP) and six neuronal progenitor domains (dp1-dp6), whereas ventral SC generates floor plate (FP) and five neuronal progenitor domains (pMN and p0-p3). These domains express distinct combinations of transcription factors. Markers listed on the right for each ___domain are identified from scRNA-seq data of mouse SC between E9.5 - E13.567. h. UMAP of SC-related cells from integrated dataset of day 4, day 9, and day 21 µNTLS, color-coded according to time points (left) or subcluster identity annotations (right). n indicates cell number. Note that cells from SC cluster as well as those from RP and FP clusters that express HOX4-13 genes have been included in analyses in h-k. i. Dot plot showing expression of key marker genes across subclusters of SC-related cells as indicated. Dot sizes and colors indicate proportions of cells expressing corresponding genes and their averaged scaled values of log-transformed expression, respectively. j. Feature plots showing average expression of indicated markers associated with each SC progenitor ___domain in UMAP plots of SC-related cells. k. Heatmap of average relative expression (Z-score) of top-20 gene signatures distinguishing each cell subcluster in SC-related cells. For gene signature information, see Supplementary Table 1.
