Figure 6.

Visualization of clusters generated from single-nucleus and single-cell RNA sequencing analyses

(A) Visualization of clusters generated from single-cell and single-nucleus data colored according to assignment by clustering analysis.

(B) Nuclei/cells visualized according to cell type and growth conditions. H1_BAP_D8_20pcO2_Khan (pink), H1_BAP_D8_5pcO2_Khan (purple), nCT (H9_nCT_D5_Io and H9_nCT_D10_Io) (yellow), and nTE (H9_nTE_D2_Io and H9_sc.nTE_D3_Io) (green) are shown. Each dot represents a nucleus/cell.

(C and D) The cell enrichment bar plots for the marker genes of clusters 6 and 8 (genes with |fold change| ≥ 1.5 and padj ≤ 0.05) along with the composition of nuclei/cells for different treatments (as percentages, relative to the total number of nuclei/cells in the condition) (see Figure S6 for cell composition of other clusters). The cell enrichment results were done using the Vento-Tormo et al. dataset, the Xiang et al. dataset, and the combined Zhou et al. and Petropoulos et al. datasets (curated by Castel et al.). Only the three most-enriched fetal cell types are shown here (see Figure S6 for the full cell enrichment results).