Extended Data Fig. 4: Survey of inhibitory neuron initial classes in the developing pig and ferret brain.
From: Conservation and alteration of mammalian striatal interneurons
a. UMAP coloured by inhibitory neuron initial classes in the E73 and E83 developing pig brain (n = 80,278 inhibitory neurons). b. UMAP coloured by batch. c. UMAP coloured by region of dissection. d. Heat map of selected markers of inhibitory initial class markers, normalized. Bar plot indicates proportion of cells from cortical and striatal dissection in each initial class. e. UMAP coloured by markers of MGE_CRABP1 initial classes, scaled and normalized. f,g. Differential expression analysis using pyDEseq2 two-sided Wald test, with adjustments for multiple comparisons using Benjamini-Hochberg method for (f) MGE_CRABP1/TAC3 initial class from cortical and striatal dissections (striatum: n = 1,430 cells, cortex: n = 246 cells), (g) MGE_CRABP1/MAF initial class from cortical and striatal dissections (striatum: n = 1,965 cells, cortex: n = 518 cells). h. Heat map of MGE_CRABP1/TAC3 and MGE_CRABP1/MAF initial classes by region of dissection, gene expression is normalized and scaled. i. Slingshot pseudotime calculation. j. Reconstruction of lineage trajectories with circles visualizing cell-type connections calculated using Slingshot. k. UMAP coloured by inhibitory neuron initial classes in the P1, P5, and P14 developing ferret brain (n = 80,278 inhibitory neurons). l. UMAP coloured by batch. m. UMAP coloured by region of dissection. n. Heat map of selected markers of inhibitory initial class markers, scaled and normalized. Bar plot indicates proportion of cells from cortical and striatal dissection in each initial class. o. UMAP coloured by markers of MGE_CRABP1 initial classes, scaled and normalized. p. Matrix plot of selected MGE_CRABP1 markers and initial class annotation of ferret within integrated dataset. q. Dot plot of MGE_CRABP1/TAC3 initial class gene expression, by region of dissection (striatum: n = 724, cortex: n = 58). r. Slingshot pseudotime calculation. s. Reconstruction of lineage trajectories with circles visualizing cell-type connections calculated using Slingshot.
