Extended Data Fig. 1: Hi-M allows high-resolution chromatin tracing in the doc-TAD.
a, Schematic representation of the genomic positions of barcodes for the low (green) and high (red) resolution doc Hi-M libraries. Triangles demarcate the two TADs registered in this genomic region90. b. Chip-seq profiles for architectural proteins in the doc-TAD54,90. Cis-regulatory modules (CRMa-d) from Fig. 1c are highlighted by blue bars. c. Typical maximum intensity projection displaying the fluorescence emission signal from a single barcode in a section of an embryo (outline in red). Emissions from individual barcodes appear as diffraction-limited spots. d. Map of pairwise distance distributions for all barcode combinations. The order of the distributions follow that in the Hi-M matrix (Fig. 1f). Blue shade represents a kernel density estimation with a bandwidth of 0.2 μm, red line represents the maximum of the distribution, and black vertical lines on the x-axis represent individual data points. e. Efficiency of barcode detection and distribution of number of barcodes detected per cell. f. To verify that uneven barcode efficiencies did not affect our results, we plotted the pairwise distance distributions for the full dataset (right) and half the data (left, here cells were randomly chosen). Map of pairwise distributions is centered at the barcode bin (4,13). g. Hi-M contact probability map (left) and inverse pairwise distance map (right) for the same experiment (doc-TAD, all cells). N = 37129, n = 29. h, Pearson correlation coefficient of the contact probability of the full doc-TAD Hi-M dataset (nc14, dorsal cells displaying doc1 expression) against subsets with a fraction of cells. One hundred random subsets were generated for each tested subset size. The central bar indicates the mean and the error bars indicate the extreme values of the distribution. i. Distribution of radii of gyration for the doc-TAD calculated from single cells. Blue shade represents a kernel density estimation with a bandwidth of 0.1 μm, black vertical lines on the x-axis represent individual data points. Dashed line represents the maximum of the distribution. The size of the doc-TAD, as estimated from its radius of gyration (0.27 ± 0.1 μm), was comparable with that of TADs of similar genomic sizes96.
