Extended Data Fig. 2: Cell quality check after infection, replicate consistency of Hi-C 3.0, and the increase of trans-chromosomal interactions after infection.
a. Representative confocal images of Mock and SARS-CoV-2 infected cells (24hpi, 0.1 MOI) stained with an antibody against the Spike protein of SARS-CoV-2 (S protein, red), and by the TUNEL assay (green). b,c. Quantification of rates of apoptosis and infection from panel a. From left to right, quantifications were conducted n = 4, 5, 3 (for panel b) and n = 4, 5, 3 (for panel c). d,e. Barplots showing the SCC correlation coefficients49 between two Hi-C replicates of Mock or SARS-CoV-2 conditions for different chromosomes. f. Snapshots showing two replicates of Hi-C contact matrices and compartmental score (E1) tracks in the same genomic region shown in Fig. 1b. The left two matrices show data of replicate 1 (rep1), and the right two matrices show replicate 2 (rep2). Green boxes show two regions with increased A-B compartmental mixing or weakened A compartment after virus infection. Bin size = 80 kb. Color scales indicate Hi-C contact frequencies. g. A heatmap shows the log2 fold change of inter-chromosomal interactions between any two chromosomes (SARS-CoV-2/Mock). h. A barplot showing the trans/cis Hi-C contacts ratio in two biological replicates of Hi-C in Mock or SARS-CoV-2 infected cells (n = 2). Trans contacts indicate chromatin interactions formed in between two different chromosomes.
