Fig. 2: Spatiotemporal dynamics of transcriptome and chromatin accessibility of the mouse and human brain cortical layers.

a, CODEX images of the mouse brain coronal sections from P0 to P21. Scale bar, 500 μm. b, CODEX staining of delineated cortical layers in the region of interest indicated by dashed rectangles in a. SSp, primary somatosensory area. Scale bar, 250 μm. c, Schematic of the spatiotemporal regression model on mouse brain cortical layers. d, Different cell types in cortical layers (S2) from the spatial RNA data. Epend, ependymal; Ex, excitatory; In, inhibitory; Mac, macrophages; MG, microglia; neu, neurons; NIPC, neuronal intermediate progenitor cell; MSN, medium spiny neurons; Cajal R, Cajal–Retzius cells; Mig Int Neu, migrating interneurons. e, The 15 RNA clusters generated from the regression model (S2). f, The 10 ATAC clusters generated from the regression model (S2). g, Representative genes in the cortical layers. h, RNA gene expression (top) and the ATAC GAS (bottom) calculated on the basis of the regression model for specific genes in mouse brains, segregated into groups based on variance of ATAC GAS in comparison to RNA expression. i, RNA gene expression (left) and the ATAC GAS (right) calculated on the basis of the regression model for specific genes in mouse brains. j, RNA gene expression (top) and the ATAC GAS (bottom) for myelination-related genes from the regression model. k, Representative gene expression (top) and ATAC GAS (bottom) for human brains, segregated into groups based on variance of ATAC GAS (bottom) in comparison to RNA expression (top). 2nd, second trimester; 3rd, third trimester. l, Representative RNA gene expression (top) and ATAC GAS (bottom) for oligodendrocyte-lineage-associated and myelination-associated genes through human V1 cortical development.