relb  (Cell Signaling Technology Inc)

Journal: Cell discovery

Article Title: NF-κB RelB suppresses the inflammatory gene expression programs of dendritic cells by competing with RelA for binding to target gene promoters.

doi: 10.1038/s41421-024-00767-9

Figure Lengend Snippet: Fig. 2 Loss of RelB leads to elevated RelA binding to a subset of genomic κB sites. a Histogram of log2FC (RelB−/−/WT) in RelA binding (RPKM) for all ChIP peaks with RPKM > 10. Descriptive statistics: mean, log2FC = −0.03; 90th percentile, log2FC = 0.62; 10th percentile, log2FC = −0.74. b Heatmap of z-scored RelA- and RelB-ChIP peaks (RPKM) in all RelB-bound peaks in WT and RelB−/−BMDCs. Peaks selected for all LPS (10 ng/mL)-induced RelB-ChIP binding events (log2FC > 1) at 1 h LPS stimulation time point in WT BMDCs, RPKM > 10 in any condition. Heatmaps for RelA- and RelB-ChIP-seq data are ordered by RelA k-means clustering and separately z-scored. c Scatter plot showing the means of log2FC (RelB−/−/WT) in RelA binding for clusters A–C from b. d Top de novo motif analysis results for genomic regions from clusters A–C from b.

Article Snippet: ChIP sample generation and data preprocessing ChIP-seq was performed as previously described81,82 with anti-RelA antibody (Cell Signaling Technology, D14E12 or Cat# 8242) or RelB antibody (Cell Signaling Technology, D7D7W or Cat# 10544).

Techniques: Binding Assay, ChIP-sequencing

Journal: Cell discovery

Article Title: NF-κB RelB suppresses the inflammatory gene expression programs of dendritic cells by competing with RelA for binding to target gene promoters.

doi: 10.1038/s41421-024-00767-9

Figure Lengend Snippet: Fig. 3 Elevated RelA binding to promoter regions is correlated with elevated gene expression. a Histogram of filtered highest FC RelA-ChIP peaks for all genes. Peaks were annotated to the nearest gene promoter region and filtered for the highest log2FC (RelB−/−/WT) in RelA binding (RPKM) for each individual gene; all peaks are RPKM > 10. Descriptive statistics: mean, log2FC = 0.24; 90th percentile, log2FC = 0.66; 10th percentile, log2FC = −0.22. b Scatter plot showing the log2FC (RelB−/−/WT) in RelA binding (RPKM) at 1 h LPS stimulation compared to all CpG-induced genes (Log2FC > 1) in WT or RelB−/−BMDCs, 8 h gene expression time point shown. Previously characterized IFN-independent hyper-expressed genes in RelB−/−are highlighted in red, and all other induced genes are colored gray. c Scatter plot comparing the log2FC (RelB−/−/WT) in RelA binding (RPKM) of IFN-independent hyper-expressed genes and genes with unchanged expression (−0.1 < log2FC < 0.1) in RelB−/−relative to WT at 8 h CpG stimulation time point. d Representative genome browser tracks for ChIP peaks near promoter regions of TSS for IFN-independent hyper-expressed genes in RelB−/−. IGV tracks from WT BMDCs are represented in blue, and IGV tracks from RelB−/−

Article Snippet: ChIP sample generation and data preprocessing ChIP-seq was performed as previously described81,82 with anti-RelA antibody (Cell Signaling Technology, D14E12 or Cat# 8242) or RelB antibody (Cell Signaling Technology, D7D7W or Cat# 10544).

Techniques: Binding Assay, Gene Expression, Expressing