Table 1.

Analysis of the epigenome: recent methods for single cell or ultra-low-input assays

Assay	Developer	Input material
Nano-ChIP-seq	Adli and Bernstein 2011	10,000 cells for H3k4me3 histone mark
Linear DNA amplification (LinDA)	Shankaranarayanan et al. 2011	For transcription factors using 5000 cells and for the H3K4me3 histone modification using 10,000 cells
Ultra-low-input micrococcal nuclease-based native ChIP (ULI-NChIP)	Brind’Amour et al. 2015	10,000 for histone marks
ChIPmentation	Schmidl et al. 2015	For several histone marks 10,000 cells per IP, and 100,000 cells for transcription factors
Single-cell ChIP-seq	Rotem et al. 2015	One cell. ChIP-seq for H3k4me3 and H3k4me2
Single-cell reduced-representation bisulfite sequencing scRRBS	Guo et al. 2015	One cell. Non-targeted enrichment DNA methylation analysis
Low-input and single-cell whole-genome bisulfite sequencing (μWGBS, scWGBS)	Farlik et al. 2015	High-throughput bisulfite sequencing assay for low-input and single-cell samples
Single-cell bisulfite sequencing scBS-seq	Smallwood et al. 2014	One cell. Targeted enrichment DNA methylation analysis