scNanoCOOL-seq

Source code for manuscript entitles scNanoCOOL-seq: a long-read single-cell sequencing method for multi-omics profiling within individual cells.

Overview

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scNanoCOOL-seq technology mainly uses bisulfite conversion and single-barcode PCR amplification strategies and finally obtained DNA fragments of approximately 900 bp in length. As shown below, the experimental process of scNanoCOOL-seq mainly includes:

1. cell lysis in a gentle way and in vitro methylation by DNA transferase M.CviPI enzyme, followed by nucleocytoplasmic separation of single cells;
2. 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;
3. the cytoplasmic part of the single cell is used for scRNA-seq library construction (optimized STRT-seq).

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Content

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• bin/: functions used in each section from pre-processing to downstream analysis
• data/: example data provided to reproduce the result
• reference/: necessary files as the reference
• vignettes/: brief introductions for each section

Data

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The raw data is accessible at SRA BioProject PRJNA905717. Parsed data is provided upon request.

Citation

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Please cite PMID: 37700167

Contact

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• Computational analysis: Xiaohui Xue (xxhui@stu.pku.edu.cn)