Extended Data Fig. 2: Comparison of 3DRAM-seq with other methods.

(A) Pairwise correlation matrixes displaying Spearman’s correlation coefficient as well as scatterplot between different RNA-seq datasets. (B) Distribution of reads across genomic features. (C) Representative examples of RNA coverage comparisons across two long, multi-exon genes. (D) Same as A but for DNA accessibility (bin size 10 kb) datasets. (E) GpC methylation levels across different ChromHMM features (n refers to the number of GpC sites analyzed per feature). (F) Venn diagram with numbers of overlapping ATAC-seq, DHS and 3DRAM-seq GpC peaks. (G) Nucleosome occupancy profiles centred at either 3DRAM-seq GpC, ATAC-seq or DHS peaks. Shown is also the profile at randomly shuffled regions as control. (H) Heatmaps showing accessibility measured by GpC methylation, ATAC-seq, DHS, as well as nucleosome occupancy (MNase-seq) across DHS peaks (I) Same as A but for DNA methylation (bin size 10 kb) (J) Heatmaps displaying methylation levels measured by different methods at individual motif centered CTCF peaks (50 bp bin size). (K) Contact probability in logarithmic bins. Lines: mean values from different methods; semitransparent ribbons: SEM. (L) Average contact enrichment at pairs of 250 kb loci arranged by their eigenvalue (shown on top). Numbers represent the compartment strength.