Extended Data Fig. 2: Quality control and integration of brainstem organoids time course scRNA-seq data.
a, Unintegrated UMAP representation of developing brainstem organoids, colored by collection day. Bargraph (upper left) depicts the contribution of each day to the final dataset. b, Violin plots showing the number of genes, number of counts, percentage of mitochondrial genes and percentage of ribosomal genes after filtering on a sample-by-sample basis. Box plots inside violin plots show the median (center line, 50th percentile), the box spans the interquartile range (25th–75th percentiles), whiskers extend to the most extreme observations within 1.5×IQR of the quartiles (defining the plotted minima and maxima). c, scIB integration benchmarking of different assessed integration methods, showing metrics for preservation of biological variation and batch correction. d, scPoli latent embedding of brainstem organoid cells, colored by timepoint (top) and snapseed annotation (bottom). e, scPoli integrated UMAP of brainstem organoids, colored by timepoint. f, scPoli integrated UMAP representation showing three age bins, early (day 5 – day 20), mid (day 30 – day 60) and late (day 90 – day 120). g, Matrixplot of scPoli (HNOCA34) or scANVI (HDBCA35) mediated label transfer annotation compared to the final annotation. For panels a-g, n = 84 organoids in total with 5-24 organoids pooled per timepoint, see Supplementary Table S1 for details.
