Extended Data Fig. 4: Batch effect assessment on organoids by split organoid experiment.
From: Deterministic scRNA-seq captures variation in intestinal crypt and organoid composition
(a) UMAP embedding of cells collected from nine additional individual organoids (under maintenance conditions) for the purpose of evaluating batch effects. Left: All 748 processed cells clustered with k-means clustering, after which clusters were annotated according to marker gene expression. Right: Expression dot plot of selected marker genes. (b) Projection of cells (colored by cell type) derived from one organoid that was split into two independent samples (split organoid) on the reference UMAP shown in a). Organoid ‘S2_2’ was split into two batches, which were processed subsequently, with a one-hour delay, during which the second batch was stored at 4 °C.
