Extended Data Fig. 4: Characterization of RNAPII ChIA-Drop data.

a, Comparison of 2D contact maps between ChIA-Drop and RNAPII ChIA-Drop replicates 1 and 2, in a 1.8-Mb segment of chromosome 3L. TADs called in ChIA-Drop data are shown in 2D contact maps, along with the tracks of histone marks H3K27ac and H3K27me3, and RNA-seq, to illustrate the active and inactive regions. The complex clusters of RNAPII ChIA-Drop data are shown at the bottom. Notably, contact signals in RNAPII ChIA-Drop data were enriched in active regions but reduced in inactive regions. b, Distribution of contact distances by GEM complexity of fragment number. The empirical cumulative distribution function of the log₁₀ of contact distances supports the pattern that small complexes have larger contact distances than large complexes. Colour scales for each curve were from the spectrum of blue to red for fragment numbers 2 to 50, in ascending order. F#, number of fragments per complex. c, Basic browser view in a 37-kb window (chromosome 2R: base pairs 5,423,000 to 5,460,000) to display the loops and peaks from two replicates of RNAPII ChIA-Drop data. Multiple ChIA-Drop fragments (n = 79) of chromatin complexes (n = 26) are shown in the bottom panel. d, Scatter plot shows peak (n = 14,347) correlations between the two replicates, inside RAID regions. Pearson correlation coefficient, r = 0.92. e, Venn diagram shows the loop anchor overlap between the two replicates, inside RAID regions. PET count cut-offs for loop numbers are indicated.