Extended Data Fig. 1: Nuclei quality control (QC) and clustering.

Number of doublets identified across all 23 datasets by DoubletDecon, DoubletFinder, and Scrublet. Red outline indicates the subset of barcodes called as doublets that were removed. b, Total number of nuclei per dataset before (yellow) and after (green) QC. c, Mean number of reads per nucleus (y axis) by dataset before QC split by age group (x axis). p value determined by two-tailed Welch’s t-test. d, Number of nuclei (y axis) by sample after QC split by age group (x axis). p value determined by two-sided Brunner-Munzel permutation test. e, Violin plots showing the number of unique molecular identifiers (UMIs) (top) and the number of genes detected (bottom) per nucleus per sample after QC. Black dots indicate the median value. Error bars show 95% confidence intervals. f, g, Median number of UMIs (2,263 pediatric and 2,011 adult) (f) and the median number of genes (1,372 paediatric and 1,226 adult) (g) detected per nucleus (y axes) by sample after QC split by age group (x axis). p values determined by two-tailed Brunnermunzel permutation test. h, UMAP plot for the 23 datasets prior to integration. i, UMAP plot showing the resulting clusters determined by the shared nearest neighbour algorithm. Data in all box plots represent mean ± sem for six paediatric and six adult samples. No significant differences were detected between pediatric and adult samples. B, biological replicate; NS, not significant; T, technical replicate. See also Supplementary Table 2.