Fig. 4: Genomic regulatory networks of cortical cell types using Projection-TAGs.
From: Projection-TAGs enable multiplex projection tracing and multi-modal profiling of projection neurons
a Pie chart categorizing snATAC-seq peaks based on their genomic locations. b Overlapping of celltype-specific peaks and projection-specific peaks in snATAC-seq data. c Analytical workflow of identifying putative enhancers and silencers and their regulated genes. d–g Heatmaps showing celltype-specific pu.Enhancers (d) and pu.Silencers (e), projection-specific puEnhancers (f) and pu.Silencers (g) and their regulated genes. Left heatmaps show the average accessibility of peaks (row) in individual defined populations (column) in snATAC-seq data, and right heatmaps show the average expression of genes (row) in individual populations (column) in snRNA-seq data. Color bars indicate the population in which the peak and gene have highest accessibility and expression, and the bar plot shows the Pearson correlation coefficient (R) between the peak accessibility and gene expression across defined populations. h Top: Scatter plot showing the correlation between the average accessibility of peak chr19-39,185,083-39,185,986 in snATAC-seq and the average expression of gene Htr7 in snRNA-seq in individual cell types (chromatin accessibility and gene expression are normalized to their max values). The dotted line represents the line of best fit. Bottom left: chromatin accessibility at the genomic locus of chr19-39,185,083-39,185,986, displayed as the average fraction of transposase-sensitive fragments per nucleus in each cell type (grouped by 50 bins per displayed genomic region). Accessibility at each locus (y-axis) is scaled to the max value across all cell types. Bottom right: expression of Htr7 in each cell type. i Top: Scatter plot showing the correlation between the average accessibility of peak chr13-82,081,120-82,082,049 and the average expression of gene Polr3g in nuclei positive for each Projection-TAG (chromatin accessibility and gene expression are normalized to their max values). Bottom left: chromatin accessibility at the genomic locus of chr13-82,081,120-82,082,049, displayed as the average fraction of transposase-sensitive fragments per nucleus in nuclei positive for each Projection-TAG (grouped by 50 bins per displayed genomic region). Bottom right: expression of Polr3g in nuclei positive for each Projection-TAG. Colors indicate the injection site of the corresponding TAG. Nuclei positive for SCL- and SCS-TAGs are combined for visualization due to low cell number.
