Fig. 1

Study design, metrics, and correlation between modalities. A Summary of the study design. B UMAP of RNA-seq data, counts from DESeq2. C UMAP of the ATAC-seq data, counts from DiffBind. D UMAP of the Hi-C loops data. E Multidimensional scaling plot (MDS) of HiCRep analysis of the Hi-C data. F Pearson’s correlation between gene expression and insulation score of the bin overlapping promoter of the gene for genes that were differentially expressed between CD4 and CD8 cells. Each dot is a gene. G Pearson’s correlation between gene expression and loop strength. Left: comparison for loops that surround the gene vs loops that are nearby the gene. Right: comparison between loops that surround the gene with loops for which loop anchor overlaps the promoter of the gene. H Pearson’s correlation between the height of ATAC-seq peaks and loop strength. Left: Comparison between loops that surround the peak vs loops that are nearby the peak. Middle: Comparison between loops that surround the peak with loops for which loop anchor overlaps the peak. Right: Comparison between loops that are nearby the peak and loops that are more than 250 kb away