Supplementary Fig. 2: Reproducibility of GRID-seq libraries.

(a) Smoothed scatter plots of uniquely mapped RNA read levels for all genes between replicated libraries of B6 (left) and F123 mESCs (right). (b) Smoothed scatter plots of uniquely mapped DNA read levels for all 10-kb genomic bins between replicated libraries of B6 (left) and F123 mESCs (right). (c) Smoothed scatter plots of background signals over all 10-kb genomic bins (B values) between replicated libraries of B6 (left) and F123 mESC (right). (d) Smoothed scatter plots of foreground signals over all 10-kb genomic bins (V values) between replicated libraries in B6 (left) and F123 mESC (right). (e) Overlapping of chromatin-associated RNAs identified in replicated and combined B6 mESC datasets. The numbers on the plot indicate the chromatin-associated RNA species in respectively coloured areas in the Venn diagram (for example: 505 common chromatin-associated RNAs are identified in the combined, replicate 1 and replicate 2 datasets; 13 chromatin-associated RNAs are identified in the combined and the replicate 2 data but not in the replicate 1 data). (f) Overlapping of chromatin-associated RNAs identified in replicated and combined F123 mESC datasets, displayed in a similar manner as in e. (g) RNA–chromatin interactome on chromosome 11 independently constructed from B6 mESC replicates. Boxed regions in each panel were enlarged with increasing resolution in the next panel on the right. A set of representative chromatin-associated RNAs are labeled on the right. (h) Interactome on chromosome 2 independently constructed from F123 mESC replicates similar to g.