Extended Data Fig. 3: O-LIT with 36plex-5K to interrogate genome organization.
From: 3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing
a, Chromosome traces of Cell 611 after Tier 2 detection of cell 611 after four rounds of O-LIT 36plex-5K off of both streets. 59/66 (89%) of 36plex-5K targets were detected. Image is from the first round of O-LIT with target identities. n = 1. b, Ball and stick of Cell 611. Colored spheres represent chromosomal targets, while black spheres represent targets that were not detected and, thus, were placed by calculating the median proportionate distance between flanking detected targets. Beginning of chromosome (for example 2pR1) marked by an asterisk. c, Single-cell pairwise spatial distance matrix after Tier 1 (top) and Tier 2 (bottom) detection of the nucleus in Fig. 3. Targets are represented on the x-axis with homologs separately displayed. Undetected targets are represented by grey lines. d, Single-cell pairwise spatial distance matrix after Tier 1 (top) and Tier 2 (bottom) detection of Cell 611. Targets are represented on the x-axis with homologs separately displayed. Undetected targets are represented by grey lines. e, 36plex-5K population pairwise spatial distances (top, from Fig. 3f). Average pairwise spatial distances from cell population after Tier 1 detection (n = 611 from 15 replicates). (Spearman’s rank correlation 0.705, two-sided p-value for a hypothesis test whose null hypothesis is that two sets of data are uncorrelated = 1.77e-174). Measurements from homologous targets were combined. Bottom, Hi-C data of 36plex-5K targets obtained from (Nir et al. 2018). f, Average distances between the nuclear membrane and the closest of the six targets imaged for each chromosome. (n = 686, 668, 364, 586, 760, and 494 for Chr2, 3, 5, 16, 19, and X, respectively.) The thick line in each violin plot represents the Interquartile range (IQR), the white dot marks the median and the thin lines extend 1.5 times the IQR.
