The Guide to DAF-seq

DAF-seq (Deaminase-Assisted single-molecule chromatin Fiber sequencing) is a method that enables single-molecule footprinting at near-nucleotide resolution while synchronously profiling single-molecule chromatin states and DNA sequence. It leverages SsDddA, a nonspecific cytidine deaminase from Simiaoa sunii, to selectively stencil single-molecule protein occupancy on intact nuclei. DAF-seq is compatible with both PacBio HiFi and Oxford Nanopore sequencing platforms, and a single-cell version (scDAF-seq) is also available.

The method is described in:

Swanson, Mao, Mallory, Vollger, Bohaczuk, Oliveira, Lyon, Ranchalis, Parmalee, Cohen, Bennett & Stergachis. Mapping single-cell diploid chromatin fiber architectures using DAF-seq. Nature Biotechnology (2025). DOI: 10.1038/s41587-025-02914-3

Quick start

  • Running the experiment? Start with the DAF-seq Protocol for the complete wet lab workflow.
  • Analyzing data? Jump to the DAF-QC Pipeline for computational setup and quality control.
  • New to DAF-seq? See the Glossary for definitions of key terms.

What's here

Wet Lab

  • DAF-seq Protocol -- Complete protocol for nuclei isolation, on-nuclei cytosine deamination, and DNA extraction
  • Primer Design -- Guidelines for designing primers for targeted DAF-seq
  • Protein Purification -- Purification protocols for SsDddA and DddI

Dry Lab

  • DAF-QC Pipeline -- Snakemake pipeline for quality control and initial processing of DAF-seq data

Reference

  • Glossary -- Definitions of key DAF-seq terms and concepts
  • Cite -- Citation information and BibTeX entry

Contributing

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For questions or contributions, see the relevant GitHub repositories: