Fig. 1

Epigenomics and the spectrum of single-cell sequencing technologies. The diagram outlines the single-cell sequencing technologies currently available. A single cell is first isolated by means of droplet encapsulation, manual manipulation, fluorescence-activated cell sorting (FACS) or microfluidic processing. The first examples of single-cell multi-omic technologies have used parallel amplification or physical separation to measure gene expression (scRNA-seq) and DNA sequence (scDNA-seq) from the same cell. Note that single-cell bisulfite conversion followed by sequencing (scBS-seq) is not compatible with parallel amplification of RNA and DNA, as DNA methylation is not conserved during in vitro amplification. Single-cell epigenomics approaches utilize chemical treatment of DNA (bisulfite conversion), immunoprecipitation or enzymatic digest (e.g., by DNaseI) to study DNA modifications (scBS-seq and scRRBS), histone modifications (scChIP-seq), DNA accessibility (scATAC-seq, scDNase-seq), chromatin conformation (scDamID, scHiC)