scNanoCOOL-seq is a sequencing method based on nanopore sequencing platform, which involves bisulfite conversion and adopt a single-barcode PCR amplification strategy. Up to now, its DNA fragments is approximately 900 bp in length. As shown below, the experimental process of scNanoCOOL-seq mainly includes:
- Preprocess: cell lysis in a gentle way and in vitro methylation by DNA transferase M.CviPI enzyme, followed by nucleocytoplasmic separation of single cells;
- DNA methylome: the nucleus of single cells is processed with single-linker amplification after bisulfite treatment and PBAT-like library construction and is used for single-molecule sequencing on the nanopore platform;
- RNA transcriptome: the cytoplasmic part of the single cell is used for scRNA-seq library construction (optimized STRT-seq).
bin/: functions used in each section from pre-processing to downstream analysisreference/: necessary files as the referencevignettes/: brief introductions for each section
The raw data is accessible at SRA BioProject PRJNA905717.
Processed data is provided upon request.
If you use scripts or code in your research, please cite:
Lin J, Xue X, Wang Y, et al. scNanoCOOL-seq: a long-read single-cell sequencing method for multi-omics profiling within individual cells. Cell Res. 2023;33(11):879-882. doi:10.1038/s41422-023-00873-5
Xiaohui Xue ([email protected])