(
A) Venn diagram comparison of GR peak sets from ChIP-seq replicates in BMDM treated as indicated (left) and between treatments (right). The union of peak sets was constructed for each condition. Read counts were determined for each peak in condition-specific peak union sets for each replicate; a plot of log transformed per peak read counts for GR replicas is shown for each treatment condition; r
s - Spearman’s correlation between replicas (left, bottom). (
B) The centrality enrichment analysis of binding motifs identified by
ab initio prediction with MEME was performed using CentriMo program of MEME suite. Significant distribution profiles relative to the peak midpoint are shown for several subsets of peaks identified by GR and p65 ChIP-seq. Left: GR-unique peaks from GR:p65 cistromes in LPS + Dex treated BMDM (
Figure 1B). Middle: GR, L + D peaks overlapping p65, L + D peaks. Right: GR, D peaks overlapping GR, L + D peaks (
Figure 1C). (
C) Distribution of gene and intron length in Dex-repressed genes compared to all expressed genes in mouse BMDM. (
D) Cross-correlation plots for GR ChIP-seq datasets generated in this study. Relative strand cross-correlations were calculated using CLC BIO Genomics Workbench.