Extended Data Fig. 3: Single cell RNA sequencing of median eminence and a size-matched region of somatosensory cortex reveals unique cell types in each brain region.

(a) Bar plot showing distribution of cells in each cell type for each experimental replicate. Replicates 12–15, in bold, are from the ME region only. (b) Bar plot showing distribution of cells in each cell type for each library batch preparation. Batch 9, highlighted in bold, is comprised of libraries from the ME region only. (c) Dot plot showing average expression of one cell type-specific transcript used to annotate cluster cell types in Fig. 2. Additional transcripts used for annotation are detailed in Methods. (d) Tukey box and whisker plot depicting the number of genes detected per cell in all identified clusters in Fig. 2. Box shows the median and first and third quartiles, whiskers represent 1.5 times the interquartile range. The cell number in each cluster per sample region is indicated at the right of each plot, with cortex-enriched clusters highlighted in red and ME-enriched clusters highlighted in blue (as determined in (e)). Data was collected on 15 separate days, with two technical replicates from ME and cortex samples in each replicate (except for replicates 12–15, which were ME only). ME and cortex regions were isolated from the same 5 mice in each replicate and pooled by region prior to dissociation. (e) Point-range plot showing the relative differences in cell proportions for each cluster in (d) between the ME and cortex. Regional enrichment was determined by permutation test, with significance assessed by false discovery rate following bootstrapping (implemented by the scProportionTest R package). Clusters showing regional enrichment (log₂ fold-change greater than |4.5| and FDR < 0.05) are labeled and shown in red.