Table 1.

Single-cell multi-omics techniques for genomic profiling together with their specific applications, conclusions and data sources

Method	Data source	Molecular layers	Objective and outcome(s)	Platform(s)
G&T-seq [22]	Mouse data: Array Express (EERAD-381) Human data: EGA(EGAS000 01001204).	192 Genomic DNA and 192 full-length mRNA sequencing in over 220 single cells from mice and humans.	To dissect genetic variation and its effects on gene expression. Cellular properties could not be inferred from DNA or RNA sequencing alone.	Illumina HiSeq X
DR-Seq [23]	GEO (GSE62952)	DR-Seq on E14 of mouse embryonic stem cell line and sequencing the mRNA from 13 single cells together with gDNA from 3 of these 13 cells.	To correlate DNA copy number variation to transcriptome variability among individual cells. Genes with high cell-to-cell variability in transcript numbers generally had lower genomic copy numbers, and vice versa.	Illumina HiSeq 2500
DNTR-seq [24]	GEO (GSE144296).	DNTR-seq on 607 cells from two pediatric acute lymphoblastic leukemia (ALL) cases, human colon adenocarcinoma cell line HCT116, and melanoma cell line A375 using Whole-genome sequencing, transcriptomics at single-cell resolution.	To address how genetic alterations affect transcription and identify minor subclones within leukemia patients. Tumorigenic alterations had a large impact on gene expression, whereas natural X/Y chromosome differences were largely silent.	Illumina NextSeq 500
Holo-Seq [25]	CRA001133, CRA001131	Small RNAs and mRNAs of 32 human hepatocellular carcinoma single cells.	To overcome the hurdles that currently limit scRNA-seq methods. The RNA metabolism kinetics of core genes were different from housekeeping genes.	Illumina HiSeq 2500
Wang et al. [26]	GSE 114071	Cosequencing of microRNAs and mRNAs across 19 single cells that were phenotypically identical.	To study how miRNAs modulate nongenetic cell-to-cell variability posttranscriptionally. The predicted targets mRNAs were significantly anticorrelated with the variation of abundantly expressed microRNAs.	Illumina HiSeq 2000