Table 4 Epi-single-cells technique developed for cancer studies

DNA methylation in single cells

scBS-seq

The first technique developed for methylome analysis. It degrades 90% of DNA and does not distinguish 5mC from 5hmC

scRRBS-seq

Technique for methylome analysis.Compared to scBS-seq, reduces DNA loss

MID-RRBS

RRBS in a microfluidic support, obtaining an efficient bisulfite conversion with high DNA recovery

PBAT

Technique for methylome analysis.It does not involve DNA fragmentation. This goes to reduce the loss

MRSE

Using the restriction enzymes to recognize methylation sites coupled with PCR amplification, reduced costs, and reaction times

RGM

It uses a fluorescence reporter to analyze dynamic changes in the state of endogenous methylation, discriminating completely the methylated genome from the single allele

scCGI-seq

Endonuclease-based method, which improves coverage and efficiency

scTRIO-seq

scTrio-seq that can be used to simultaneously analyze the genomic copy-number variations (CNVs), DNA methylome, and transcriptome of an individual mammalian cell

scMAB-seq

Methylome technique that use enzymes for DNA conversion. Distinguishes 5mC and 5hmC from 5fC (5-formylcytosine) and 5-caC (5-carboxycytosine)

scAba-seq

Methylome technique used to specifically detect 5hmC by restriction enzyme. It has low efficiency

DNA methylation analysis with gene expression

scMT-seq; scM&T-seq

Methylation associated with transcription

scTRIO-seq

Gene promoter and hypo- and hyper-methylation study

scNMT-seq

Nucleosome, methylation, and transcription

Single-cell histone modification sequencing

scChip-seq

Method used to analyze protein interactions with DNA

scChil-seq; scCUT&Tag-seq; scChIL-seq; scChIC-seq

Technologies that isolate the DNA sequences attached to histones with specific marks or transcription factors

scATAC-seq

Technique that gives the possibility to improve the data obtained with DNA and RNA sequencing, with the information of chromatin accessibility

scCOOL-seq

Detection of chromatin status/nucleosome localization, DNA methylation, copy number variation, and ploidy

ISH-PLA

Technique for RNA regulation study, gives information on histone modification by imaging, cell phenotype, and cell–cell interaction