Fig. 2: Spatial genome alignment of seqFISH+ chromatin imaging of mESCs at 25 kb and 1 Mb resolution.
From: A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH
a, Heatmaps of seqFISH+ chromatin imaging of mESCs at 25 kb resolution (bottom left) juxtaposed to contact frequency from bulk proximity-ligation assay or Hi-C binned at 25 kb (top right). The distance matrix is an untabulated, median distance matrix of all single-molecule chromatin fibers identified by spatial genome alignment for every chromosome across 1,160 cells. Heatmaps for 1 Mb chromatin tracing imaging data are shown in Extended Data Fig. 4. b, Spearman correlation between pairwise spatial distances (x axis, log normalized) imaged at 25 kb resolution against Hi-C contact frequency (y axis, log normalized) binned at 25 kb resolution. c, Spatial distance to proximity-ligation correlation comparison across methodologies, at 1 Mb seqFISH+ imaging resolution as well as 25 kb resolution. For 25 kb resolution where DNA domains organize nonlinearly, we note that single-molecule chromatin fiber tracing via spatial genome alignment captures structural variations more faithfully than tabulating all pairwise spatial distances within a specified radius into an ensemble structure.
