Extended Data Fig. 3: Region-specific gene expression changes across age.
From: Sensory input, sex and function shape hypothalamic cell type development
(a) UMAP across all 8 ages for inhibitory neurons. Upper, colored by cluster (key in Fig. 1c, upper); lower, colored by age. Inset: gradient across age for one cluster. (b) Mapping of E16 onto P65 clusters using canonical correlation analysis, for inhibitory neurons. Prediction score is averaged across cells within a cluster. Note that almost all E16 cell types map to a single P65 cell type, with very few off-diagonal elements. (c) Identity ratio quantifies how well clusters from young ages computationally map onto adult clusters: identity ratio of 1 denotes complete mapping to a single cluster, and identity ratio of 0 denotes equal mapping to 2 or more clusters. Each data point represents a single cluster, averaged across all cells. Data shown for excitatory cell types. Boxplots show median, interquartile range, and 1.5 * interquartile range, as well as all outliers beyond this range shown as points. (d) For excitatory neurons, correlation between pseudobulked gene expression of all clusters at E16. Colored bars on top and right indicate sub-region (excitatory sub-region key in Fig. 1d). Boxes demarcate cell types within the same POA sub-region. (e) As in (d) but at P65. Note that at P65, there are higher correlation values between clusters within the same sub-region (within the boxes, quantified in (f)) and lower correlation values between clusters in different sub-regions (between boxes). (f) For excitatory neurons, correlation between clusters within a sub-region (i.e. within the boxes in panels (d-e)), at each age, normalized to correlation at P65. ***p = 8.68 × 10−5 for one-way ANOVA, effect of age. (g-i) As in (d-f), but for inhibitory neurons. (i) p = 3.23 × 10−13, one-way ANOVA, effect of age. (j) Marker genes specific to excitatory neuron sub-regions, found at either E16 but not P65 (left) or P65 but not E16 (right), plotted for E16 cells (upper) or P65 cells (lower). (k) Using regional markers at P65 that are not markers at E16 (genes on right panel of (j)), correlation of regional expression at each age compared to P65. (l) Region-specific marker genes at E16 (upper) or P65 (lower).
