Extended Data Fig. 2: Generalizability and reproducibility of the SAMOSA-ChAAT protocol.
From: Nucleosome density shapes kilobase-scale regulation by a mammalian chromatin remodeler
a). As in Fig. 2b, but for a completely different murine sequence (‘S2’). Footprint sizes from SAMOSA-ChAAT experiments carried out at varying nucleosome densities follow closely with expected nucleosome sizes, plus expected ‘breathing’ of DNA around the histone octamer, with the extent of breathing decreasing as nucleosome density increases. b). SAMOSA-ChAAT data enables direct estimation of the absolute number of nucleosomes per footprinted S2 fiber. c). Footprint length vs. midpoint ‘horizon’ plots for footprinted S2 fibers. d). UMAP dimensionality reduction of S2 fiber accessibility data. e). Visualization of a subset of sampled molecules following Leiden clustering of single molecule data. f-g). Widom 601 nonanucleosomal fiber data from ref. 9 was reprocessed using the NN-HMM. Called footprints are the expected length of 601-assembled nucleosomes (f), and horizon plots reveal positioned nucleosomes at expected positions (g). h–k). Correlation of footprint abundances for S1 fibers of each density across two replicates (different salt gradient dialysis preps).
