Supplementary Fig. 1: Identification of chromatin-associated RNAs.

(a) All mouse genes were ranked in a descending fashion by their normalized RNA read densities captured by GRID-seq in B6 mESC datasets. Each dot represents one gene and red ones highlight genes with the RNA read density of >100 RPK. RPK: reads per kb. (b) Similar plot based on F123 mESC datasets as in a. (c) All genes were ranked in a descending fashion by the maximal linked DNA read density on all genomic bins in B6 mESC datasets. Each dot represents one gene and blue ones emphasize genes with DNA read density of >10 RPK. (d) Similar plot based on F123 mESC datasets as in c. (e) Scatter plot showing the distribution of all genes based on their RNA read densities (x-axis) and maximal DNA read densities over genomic bins (y-axis) in B6 mESC datasets. Red dots correspond to genes marked with red dots in a; blue dots correspond to genes marked with blue dots in c; purple dots represent chromatin-associated RNA that survived both cutoffs. (f) Similar plot based on F123 mESC datasets as in e. (g, h) Saturation analyses performed by random subsampling 5 to 55 million uniquely mapped read mates in B6 and 5 to 35 million uniquely mapped read mates in F123 mESC datasets. Each level of random subsampling was independently repeated 5 times. Numbers of chromatin-associated RNAs identified were summarized and plotted in g. The green line represents the connected mean values in B6, and the orange dotted line represents those in the F123 mESC dataset. Numbers of 1 kb-binned genomic regions that have at least 10 linked DNA reads were summarized and plotted in h. The blue line represents the connected mean values in B6, and the red dotted line represents those in the F123 mESC dataset.