Single-cell chromatin conformation capture of diploid cells by Dip-C (analyzed with the dip-c package)

To reconstruct the 3D genomes of single diploid human and mouse cells, we performed single-cell chromatin conformation capture by a novel method, Dip-C, on human cells, and re-analyzed published data on mouse cells by the Dip-C algorithm. We performed Dip-C on 17 GM12878 human lymphoblastoid cells and 18 peripheral blood mononuclear cells (PBMCs) from a male human donor, and re-analyzed published data (GSE94489) on 10 mouse embryonic stem cells (mESCs) from a hybrid mouse. For 3D reconstruction, we performed 3 replicates per human cell and 5 replicates per mouse cell. BioProject for the human data is PRJNA473369.