Fig. 2: Characterization of CREs across various brain regions of the macaque cortex.

a Diagram showing the integration and one-to-one pairing of snATAC-seq and spatial transcriptome data. b Genome browser track view showing differential accessible distal CREs linked to GPR83, ADCYAP1, RORB and TLE4 in various glutamatergic neurons. c Spatial maps and bar plots showing the chromatin accessibility of four example CREs and expression levels of these CREs-linked genes across cortical layers in a representative coronal section (EBZ + 10). The quantification was calculated from chromatin accessibility of all single nuclei in each layer, and the sample sizes are listed in Supplementary Data 10. Error bars represent standard error of the mean (SEM). d Gene regulatory networks of the V1-specific L4_2 glutamatergic neurons. Red and green colors represent TFs and their target genes, respectively. The directed edges indicate the regulation. e Genome browser track view showing a differential accessible distal CRE linked to CPA6 in various glutamatergic neurons. f Spatial maps of expression patterns of MEF2C and CPA6, and chromatin accessibility of the CRE linked to CPA6 at two representative sections (EBZ −6.3 and −6.8). g RNAscope assay showing the expression pattern of the CPA6 gene in V1 and V2 regions of the macaque cortex. Probes against CPA6 (ACD, cat#1843691-C1) was list in Supplementary Data 9. DAPI was used for nuclear counterstaining. One of two biological replicates was shown from a single experiment. Independent replicates showed consistent patterns. h Co-localization of RNAscope labeling of the CPA6 gene and the MEF2C gene in the V1 region, a magnified view in (g). i Heatmap showing the correlation of chromatin accessibility and the hierarchy levels of various brain regions in the visual and somatosensory system. Correlation coefficients and P values were calculated by Spearman correlation analysis. * P < 0.05, ** P < 0.01, *** P < 0.001. j Dot plots showing the correlation of chromatin accessibility and the hierarchy levels of various brain regions in the visual system listed in (i). k Genome browser tracks showing the chromatin accessibility of two CREs linked to CBLN2 among L2/3, L3/4 and other cell subclasses.