Table I.
Low-input and single cell methods available for assaying epigenetic modifications.
| Epigenetic layer | Assay | Low-cell protocol | Single-cell protocol |
|---|---|---|---|
| DNA methylation | Post-bisulfite adaptor tagging (PBAT) | 400 cells (Miura et al., 2012) | Yes (Smallwood et al., 2014) |
| Reduced representation bisulfite sequencing (RRBS) | 75–1000 cells (Smallwood and Kelsey, 2012) | Yes (Guo et al., 2013) | |
| Histone modifications | Chromatin immunoprecipitation (ChIP)-seq | 400–1000 cells (Brind’Amour et al, 2015, Zhang et al., 2016, Dahl et al., 2016, Hanna et al., 2018) | Yes* (Rotem et al., 2015) |
| Cleavage under targets and release using nuclease (CUT&RUN) | 100 cells (Skene et al., 2018) | Not available | |
| Chromatin accessibility | Assay for transposase accessible chromatin (ATAC)-seq | 20–100 cells (Wu et al., 2016, Wu et al., 2018) | Yes (Buenrostro et al., 2015; Cusanovich et al., 2015) |
| DNase-seq | 100–200 cells (Lu et al., 2016) | Yes (Jin et al., 2015) | |
| DNA methylation and chromatin accessibility | Nucleosome occupancy and methylome (NOMe)-seq | Not available | Yes (Pott, 2017, Guo et al., 2017a, Clark et al., 2018) |
| Higher order organisation | Hi-C | 500 cells (Du et al., 2017) | Yes (Nagano et al., 2013) |
*Only applied using thousands of cells.