Figure S4. Macrophages from a second... | Rockefeller University Press

Figure S4.

$Macrophages from a second human donor show reversibility of IFNγ-induced chromatin accessibility and de novo enhancers. Human macrophages from a second human subject were stimulated with IFNγ (100 ng/ml) for 8 h. Cells were subsequently washed and cultured for an additional 88 h in standard media or media supplemented with 1 µM ruxolitinib. ATAC and H3K4me1 CUT&Tag was performed after 8 h of stimulation and 88 h after cytokine washout. (A) Boxplot quantifying log2 fold changes of reads within IFNγ-induced ATAC peaks after 8 h of IFNγ stimulation and after washout for each condition (L2FC > 2, FDR < 0.01). (B) Heatmap of Z-scored reads within ATAC peaks induced IFNγ after 8 h of stimulation and 4 days after washout for each condition. Clusters were generated by unsupervised k-means clustering. Each column represents a biological replicate from the same human donor. (C) Boxplot quantifying log2 fold changes of reads within IFNγ-induced H3K4me1 CUT&Tag peaks after 8 h of IFNγ stimulation and after washout for each condition (L2FC > 2, FDR < 0.01). (D) Barplot showing fraction of IFNγ-induced H3K4me1 peaks at 8 h that persist 4 days after washout in each condition. Persistence was defined as L2FC ≥ 0, FDR < 0.01. (E) Heatmap of Z-scored reads within H3K4me1 peaks induced IFNγ after 8 h of stimulation and 4 days after washout for each condition. Clusters were generated by unsupervised k-means clustering. Each column represents a biological replicate from the same human donor. (F) Boxplot of log2CPM of reads within each peak for each cluster in E. Box/whisker plots indicate interquartile range and 1.5× interquartile range. Statistical tests were determined by paired Wilcoxon test. ****P < 0.0001.$

Macrophages from a second human donor show reversibility of IFNγ-induced chromatin accessibility and de novo enhancers. Human macrophages from a second human subject were stimulated with IFNγ (100 ng/ml) for 8 h. Cells were subsequently washed and cultured for an additional 88 h in standard media or media supplemented with 1 µM ruxolitinib. ATAC and H3K4me1 CUT&Tag was performed after 8 h of stimulation and 88 h after cytokine washout. (A) Boxplot quantifying log2 fold changes of reads within IFNγ-induced ATAC peaks after 8 h of IFNγ stimulation and after washout for each condition (L2FC > 2, FDR < 0.01). (B) Heatmap of Z-scored reads within ATAC peaks induced IFNγ after 8 h of stimulation and 4 days after washout for each condition. Clusters were generated by unsupervised k-means clustering. Each column represents a biological replicate from the same human donor. (C) Boxplot quantifying log2 fold changes of reads within IFNγ-induced H3K4me1 CUT&Tag peaks after 8 h of IFNγ stimulation and after washout for each condition (L2FC > 2, FDR < 0.01). (D) Barplot showing fraction of IFNγ-induced H3K4me1 peaks at 8 h that persist 4 days after washout in each condition. Persistence was defined as L2FC ≥ 0, FDR < 0.01. (E) Heatmap of Z-scored reads within H3K4me1 peaks induced IFNγ after 8 h of stimulation and 4 days after washout for each condition. Clusters were generated by unsupervised k-means clustering. Each column represents a biological replicate from the same human donor. (F) Boxplot of log2CPM of reads within each peak for each cluster in E. Box/whisker plots indicate interquartile range and 1.5× interquartile range. Statistical tests were determined by paired Wilcoxon test. ****P < 0.0001.