scNanoCOOL-seq: a long-read single-cell sequencing method for multi-omics profiling within individual cells

We developed a new single-cell muti-omics sequencing method by adapting a modified scCOOL-seq protocol to the nanopore sequencing platform, termed scNanoCOOL-seq, which could simultaneously profile the transcriptome, copy number variations (CNVs), DNA methylation, and chromatin accessibility in the same individual cell. Taking advantage of the long-range amplicons obtained from a modified protocol of post-bisulfite adaptor tagging (PBAT) and third generation sequencing platform, we found that scNanoCOOL-seq performed well in detecting the epigenetic features of full-length CpG islands (CGIs) and promoters, and structural variations (SVs) such as translocations directly, and the epigenetic features flanking the fusion point of gene BCR and ABL1 in the cell line K562 were compared between the wild-type alleles and the variants. We also demonstrated that scNanoCOOL-seq dissected the dynamics and heterogeneity of multi-omics in leukemia cells along with the treatment of 5-azacytidine (5-aza). In mammals, preimplantation embryos undergo dramatic and crucial epigenetic reprogramming and cell fate determination. We profiled 441 mouse blastocyst cells and revealed the dynamics of DNA methylation in E3.5 and E4.5 blastocysts.