Fig. 2: Single-cell RNA-seq analysis of early organoids confirms multiple neural and mesodermal lineages.

a Unsupervised cluster analysis of individual cells from early organoid cultures. Organoid cultures, three independent biological differentiation replicates of the control iPSC line 11a, were dissociated at 2 weeks in culture, and 20,835 single-cell libraries were sequenced at an average read depth of 35,000 reads/cell covering an average of 2555 unique genes/cell. The visualization shows tSNE plots of individual cells as dots and clusters of cells as colored groups. Numbers indicate cluster identity. b classification of clusters into six broad cell types. Marker genes for each cell cluster were identified, and clusters were then classified into groups accordingly. Clusters that could not be unambiguously identified are labeled as unspecified. The visualization shows the same tSNE plot from (a) recolored to reflect cell type. c Expression of cluster-defining genes enriched in each cell type classification. Marker genes that are enriched in each cluster within a cell-type classification were identified. Note that the neural progenitor cell type was defined by the presence of gene subsets from both the intermediate progenitor (OLIG3, SOX2, and DLL1) and neuronal (MAP1B, TUBB3) cell types. The plot shows the mean of scaled expression of indicated genes from within each cell cluster. High and low gene expression are indicated by cyan and magenta, respectively.