Figure 7.
Differences in cell-type-specific gene expression and chromatin accessibility in the Silc1−/− hippocampus
(A) UMAP visualization of the snRNA-seq expression data, with color coding of the 22 clusters of cells.
(B) Expression levels of Sox11, Silc1, and selected marker genes projected onto the UMAP visualization.
(C) Left: dot plot of the expression levels and the fraction of cells in which each indicated gene was expressed in each indicated cluster. Right: numbers of significantly differentially expressed genes in each cluster and the fraction of these that overlap with the “known” Sox11 targets from other studies.28,51,52
(D and E) GO cellular compartment (D) and biological process (E) terms enriched in the genes significantly downregulated in Silc1−/− cells compared with WT cells in cluster 3.
(F) Volcano plot of the difference in read coverage (x axis) and statistical significance (y axis) at the 31,764 peaks called by MACS2 using the entire dataset. Peaks in the ∼2-Mb gene desert flanking Sox11 are shown in red. The inset shows ATAC-seq read coverage in the most differential Sox11-proximal peak, which is one of the peaks highlighted in Figure S1.
(G) Changes in TF footprints for each TF family present in the JASPAR database. Motifs assigned to the indicated families are marked in one of five colors.