Fig. 2: 3D-EMISH chromatin image collection for 1.7 Mb target genomic region.
a Genome browser view of the target region in hg38, Chr7:141,547,153–143,237,066, in GM12878 cells. From top to bottom, 2D contact map (CTCF ChIA-PET, 5Kb resolution), three distinctive loop domains (141,547,153–141,786,415; 141,975,791–142,304,141; 142,463,980–143,237,066), loop and peak for CTCF ChIA-PET, loop and peak for RNAPII ChIA-PET, RNA-seq, and DNA probes using BAC clone for 3D-EMISH and two-color FISH. b Confocal microscopy image of the target genomic region using two-color DNA-FISH (left) and 3D reconstructed FISH signals (right). This experiment was repeated independently three times with similar results. c Cross-section illustration of 3D-EMISH cubical samples, where the dotted black square represents the sample boundary. Cells contain either two target chromatins in a nucleus (G1 phase) or four target chromatins in a nucleus (S-M phase). 3D-EMISH collected whole-cell nuclei (W, orange), located at the inner cubic sample, and truncated nuclei (T, blue), located at the outer cubic sample. Intact target chromatin-folding structures (green dots) were collected. Truncated partial structures and structures beyond the cubical sample were not collected, represented as red dots. Total 229 target chromatin-folding structures were collected from two replicates, containing 26 whole nuclei and 140 truncated nuclei. d Examples of collected target chromatin-folding structures with their nuclei are presented. From top to bottom, 1(T), 2(T), 2(W), 3(T), and 4(W) structures per a nucleus are shown with structure index numbers (sID, details in Source Data 1 and Supplementary Fig. 5). e Nucleus count for 1, 2, 3, and 4 structures per a nucleus.
