Table 6 Current methods available for single-cell multi-omics sequencing
From: Single-cell sequencing technology applied to epigenetics for the study of tumor heterogeneity
Technique | Technical features | Designed by |
|---|---|---|
Paired-Tag | Paired-Tag is a high-throughput genomic sequencing technology that enables simultaneous sequencing of target DNA and its adjacent regions; high throughput; relatively low cost; comprehensive sequencing information; applicability in gene structure analysis, genomic variation analysis, and chromatin conformation studies; requires rigorous primer design; complex data analysis | [155] |
Paired-seq | Paired-seq is a high-throughput sequencing technique that integrates scRNA-seq and scDNA-seq to enable simultaneous analysis of the transcriptome and genome of cells; high throughput; relatively higher costs; requires complex primer design and data analysis; | [1] |
scDAM&T-seq | scDAM&T-seq is a high-throughput sequencing technique that combines single-cell DNA adenine methylome and transcriptome sequencing; simultaneous analysis of the DNA adenine methylation and gene expression at the single-cell level; high throughput; relatively higher costs; | [156] |
sci-CAR-seq | sci-CAR-seq simultaneously analyzes the transcriptome and chromatin conformation information of individual cells; simultaneous view of gene expression and chromatin three-dimensional structure at the single-cell level; high throughput; relatively higher costs | [144] |
SHARE-seq | SHARE-seq allows for the simultaneous analysis of the transcriptome and chromatin interactions; high throughput; relatively higher costs | [145] |
SNARE-seq | SNARE-seq can simultaneously obtain transcriptome and chromatin accessibility data from the same individual cell; it is suitable for tissues that are difficult to separate into single-cell suspensions; Microfluidic-based Single-Cell Isolation and Barcoding Technology; medium to high throughput | [146] |
ASTAR-seq | ASTAR-seq is a new single-cell sequencing technology that simultaneously measures the transcriptome and chromatin accessibility of cells; multiple cells are processed at the same time in a single experiment, which improves experimental throughput; incompatible with automated platforms; may result in gene loss | [147] |
scCAT-seq | scCAT-seq, a technique for simultaneous determination of chromatin accessibility and transcriptome within the same single cell; accurate construction of regulation between cis-regulatory elements and target genes | [143] |
scMT-seq | scMT-seq is a composite sequencing technology that allows for simultaneous analysis of the genome, transcriptome, and methylome of individual cells; lower throughput, higher cost, and complex operation; reveals the interactions between different biological molecular levels within single cells | [151] |
scmCT-seq | Methylome + transcriptome | [152] |
scM&T-seq | scM&T-seq is a technology that enables the simultaneous acquisition of DNA methylation and transcriptome information from individual cells; relatively costly and technically complex | [153] |
scGEM | scGEM is a single-cell genome and epigenome sequencing technology that allows for the simultaneous analysis of the genome and epigenome of individual cells; relatively costly and technically complex; offers high throughput and reveals genetic and epigenetic heterogeneity among cells | [154] |
Pi-ATAC | Pi-ATAC combines CRISPR-Cas9 gene editing technology with ATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) to enable site-specific genome editing while simultaneously measuring the impact on genome accessibility; high throughput capacity; higher cost; technically complex | [162] |
ASAP-seq | ASAP-seq is a high-throughput sequencing technique that combines single-cell DNA adenine methylome and transcriptome sequencing; simultaneous analysis of the DNA adenine methylation and gene expression at the single-cell level; high throughput; relatively higher costs | [163] |
scNMT-seq | scNMT-seq allows concurrent profiling of nucleosome structure, DNA methylation, and transcriptome information from individual cells, providing comprehensive analysis across different cellular levels; high throughput capabilities; higher costs; technical complexity | [157] |
scNOMeRe-seq | scNOMeRe-seq is a sequencing technique that allows for the simultaneous analysis of nucleosome occupancy and DNA methylation information from individual cells; high throughput; high costs and complex data analysis; operationally and analytically complex | [158] |
scChaRM-seq | scChaRM-seq is a sequencing technique that allows for simultaneous profiling of chromatin accessibility and DNA methylation information from individual cells; high throughput; high costs; technical complexity | [159] |
snmCAT-seq | snmCAT-seq is a sequencing technique that allows for the simultaneous measurement of multiple omics information, including gene expression, chromatin accessibility, and DNA methylation, from individual cell nuclei; high throughput; utilizes a combination of multiple molecular markers, such as RNA, DNA methylation, and chromatin accessibility tags, to capture the multi-dimensional; research cell typing, cell type classification, and functional analysis; complex experimental procedures | [160] |
Smart-RRBS | Smart-RRBS can simultaneously obtain transcriptome information and copy number alteration (CNA) information; technical complexity; high throughput | |
scNOME-seq | scNOME-seq is a single-cell technology used to determine the assembly of nucleosomes and DNA methylation patterns within cells; detection of subtle variations in DNA methylation patterns; relatively low throughput; limited by sequencing depth restrictions | [164] |
scMethyl-HiC | scMethyl-HiC is a technology that combines single-cell DNA methylation sequencing with chromosome conformation capture (Hi-C) to simultaneously detect DNA methylation and chromosomal spatial structure information in individual cells; insights into the heterogeneity of DNA methylation and spatial structure between cells; relatively low throughput; higher costs; complex experimental workflow and data analysis requirements; high sequencing depth requirements and a complex experimental process | [164] |
sn-m3C-seq | sn-m3C-seq is a single-nucleus multi-omics methylcytosine and chromatin conformation sequencing technology that enables simultaneous measurement of DNA methylation and chromatin 3D structure information in individual cells; reveals the heterogeneity of DNA methylation and chromatin structure among cells, providing insights into cellular variability; relatively low throughput; higher costs; complex experimental workflow and data analysis | [165] |
scCOOL-seq | scCOOL-seq is a single-cell chromatin conformation and open chromatin sequencing technology used for simultaneously measuring the chromatin 3D structure and open chromatin regions in individual cells; low throughput; higher costs; exploration of the relationship between chromatin structure and gene regulation in individual cells; complex experimental workflow and data analysis | [166] |
iscCOOL-seq | iscCOOL-seq is an improved single-cell COOL-seq method based on the TAILS strategy. iscCOOL-seq can simultaneously analyze chromatin accessibility, DNA methylation, and gene expression; sequencing depth and coverage are limited; and sample processing and experimental manipulation are demanding | [167] |