Fig. 1: Overview of the Uni-C experimental workflow.

a Experimental workflow for Uni-C. Cells are subjected to dual crosslinking with formaldehyde and EGS, followed by cell membrane lysis to release the nuclei. Then, the nuclei are fragmented via a 4-base pair cutter restriction enzyme, and the fragments are processed via end-repair by Klenow (exo + ) polymerase and proximity ligation by T4 DNA ligase. After ligation, the tumor cell nuclei are transferred into an alkaline lysis solution using glass micropipettes, followed by single-cell amplification in a mixture containing EquiPhi29, dNTPs, and thiol-modified ddNTPs. The amplified products were then size-selected and used to construct a sequencing library for high-throughput sequencing. This process allows for the comprehensive detection of various genomic anomalies through the combined analysis of whole-genome sequencing and three-dimensional genome structural data. b Comparison of the no-duplication read pairs ratio among Uni-C, HiRES, and Dip-C (n = 10 cells per method). The ratio of non-duplicated read pairs is defined as the percentage of read pairs that are non-redundant within the total raw read pairs. In both panels, each dot represents a single-cell library. Solid horizontal lines indicate the medians, and dashed lines indicate the 25th and 75th percentiles. c Comparison of the ratio of intra-chromosomal long-range interaction read pairs between Uni-C, HiRES, and Dip-C (n = 10 cells per method). The intra-chromosomal long-range interaction read pairs ratio refers to the percentage of read pairs within the same chromosome that interact over distances greater than 10 kb within the total raw read pairs. Solid horizontal lines indicate the medians, and dashed lines indicate the 25th and 75th percentiles. Source data are provided as a Source Data file.