Extended Data Fig. 9: Transcriptomic comparison between µNTLS and neural cells from human embryonic tissues.
From: A patterned human neural tube model using microfluidic gradients
a. (Top left) UMAP showing integrated data from day 9 µNTLS and neural cells in Carnegie Stage (CS) 12 human embryos42. (Top middle & right) UMAP plots of day 9 µNTLS data and CS12 human neural cell data, separated from the integrated UMAP plot, as indicated. n indicates cell numbers. (Bottom) Feature plots comparing expression of key marker genes between day 9 µNTLS and neural cells in CS12 human embryos. b. (Top) UMAP plots of Neuron clusters in day 9 µNTLS and CS12 human embryo datasets. Neuron cluster in day 9 µNTLS dataset is projected onto the Neuron cluster in CS12 human embryo dataset and is annotated following the human reference data42 (see Methods). n indicates cell numbers. (Bottom) Feature Plots comparing expression of key marker genes between Neuron clusters in day 9 µNTLS and CS12 human embryos. c. (Top left) UMAP showing integrated data from day 21 µNTLS and neural cells in CS15-16 human embryos42. (Top middle & right) UMAP plots of day 21 µNTLS data and CS15-16 human neural cells, separated from the integrated UMAP plot, as indicated. n indicates cell numbers. (Bottom) Feature plots compare expression of key marker genes between day 21 µNTLS and neural cells in CS15-16 embryos. d. (Top) UMAP plots of Neuron clusters in day 21 µNTLS and CS15-16 human embryo datasets. Neuron cluster in day 21 µNTLS dataset is projected onto the Neuron cluster in CS15-16 human embryo dataset and is annotated following the human reference data42 (see Methods). n indicates cell numbers. (Bottom) Feature Plots comparing expression of key marker genes between Neuron clusters in day 21 µNTLS and CS15-16 human embryos. e. Pearson’s correlation analysis of cell clusters in day 9 and day 21 µNTLS with neural clusters in CS12-16 human embryo datasets42. Black boxes highlight the highest correlation coefficients in each column. Correlation coefficients between indicated µNTLS and human clusters are calculated based on variable genes identified from human neural cell clusters (Supplementary Table 1). f. Pearson’s correlation analysis of Neuron subclusters in day 9 and day 21 µNTLS with Neuron subclusters in CS12-16 human embryo datasets42. Black boxes highlight the highest correlation coefficients in each column. Correlation coefficients between indicated µNTLS and human clusters are calculated based on variable genes identified from human neural cell clusters. g. Alluvial plots showing percentages of cells for each cell cluster in day 9 and day 21 µNTLS (top) and human embryos at CS12, CS13-14 and CS15-16 (bottom). h. day 4, day 9, and day 21 µNTLS show closest transcriptome similarities with human neural cells at CS8-9 (day 17–20), CS12 (day 26–30), and CS15-16 (day 35–42), respectively42. Note that corresponding human embryo stage of day 4 μNTLS is inferred from the comparison between day 4 μNTLS and mouse data44 (See Supplementary Figs. 8–10).