Extended Data Fig. 4: Transcriptional and chromatin accessibility profiling of Arid1a-deficient activated B cells.

a-c. GSEA plots for the transcriptional profile of Cg1 Arid1a KO and control B cells, using gene sets from. Pyroptosis (a), Innate immune response (b) and IL-6 production (c) pathways. Y-axis denotes enrichment score. NES, Normalized enrichment score, FDR, False discovery rate. d. Genome browser view of RNA-seq and ATAC-seq data at Igh loci. Asterisks denote changes in accessibility (red and black asterisks denote increased and decreased accessibility signals in Cg1 Arid1a KO cells, respectively). e. Heatmap showing ATAC-Seq signals from individual replicates in differentially accessible regions identified in Cg1 Arid1a KO and control B cells. RPM values in DARs are plotted in +/− 2 kb windows from the center of the peak. f. Aggregate ATAC-seq footprint for RUNX1 and EBF1 (left); CTCF and EGR1 (right) generated over binding sites on Control DARs (left) or KO DARs (right), respectively. g. Scatter plot of log2 fold change DARs (y-axis) and gene expression changes (x-axis) between Cg1 Arid1aKO and control B cells. DEGs associated with a DAR are denoted in color (black: downregulated; red: upregulated in Cg1 Arid1a KO). h-j. Genome browser view of RNA-seq and ATAC-seq data at Socs3 (h); and Prdm1 (i) and Cd72 (j) loci. Asterisks denote regions of interest. Please see bioinformatics analysis in methods for additional information.