Fig. 5: The integrated atlas enables protocol assessment and can be extended via dataset projection.
From: An integrated transcriptomic cell atlas of human endoderm-derived organoids
a, Schematic representation showing the analytical pipelines and varied interfaces to facilitate analyzing scRNA-seq data of organoid samples for the atlas. b, Experimental design of the ileum organoid sample with TNF treatment to generate M cells. The UMAP of sample scRNA-seq data mapped to the organoid atlas is colored by predicted level 2 cell types. The bar plot shows the cell proportions of predicted level 2 cell types across control and TNF treatment scRNA-seq data. c, Experimental design of the colon organoid sample using a scaffold-guided hydrogel chip model. The UMAP of sample scRNA-seq data mapped to the organoid atlas is colored by predicted level 2 cell types and time points, with a bar plot depicting the cell proportions of predicted level 2 cell types across the time course scRNA-seq data. d, Experimental design of the lung alveolar organoid samples. The UMAP of sample scRNA-seq data mapped to the organoid atlas is colored by predicted level 2 cell types and time points, with a bar plot depicting the cell proportions of predicted level 2 cell types across the time course scRNA-seq data. e, Experimental design of the lung airway organoid samples. The UMAP of sample scRNA-seq data mapped to the organoid atlas is colored by predicted level 2 cell types and time points, with a bar plot depicting the cell proportions of predicted level 2 cell types across the time course scRNA-seq data. Ctrl, control; DE, differential expression; Neuroendo., neuroendocrine.
