Fig. 6

Projection of scRNA-seq and scATAC-seq data to reference scRNA-seq atlas using CSS. a Projection of scRNA-seq data of two Sc102a1 cerebral organoids to the reference atlas built using scRNA-seq data of the other eighteen cerebral organoids. The barplot shows the proportion of cells per organoid that are located on the dorsal or ventral telencephalon or diencephalon, mesencephalon, and rhombencephalon (D/M/R) neuronal trajectory. b UMAP embedding of the reference atlas based on CSS representation. Cells are colored by cell type annotation (left). Cells in the Sc102a1 organoids are projected to the reference atlas with cells in the projected embedding colored by their previous (see Fig. 2) cell type annotation (middle). Proportion of cells for which the predicted cell type is consistent or inconsistent with the previous annotation is shown in the barplot (right). c Projection of scATAC-seq data of dissected cortex-like areas in cerebral organoids to the scRNA-seq reference atlas including twenty cerebral organoids. Projected loci of cells in the scATAC-seq data set is shown in the reference UMAP embedding, colored by the independent cell type annotation. Pie charts show the proportion of cells in the scATAC-seq data set projected to dorsal, ventral, or D/M/R neuronal branches (top right), the cell type composition of cells predicted as NPCs (middle right), and the cell type composition of cells predicted as neurons (bottom right)