Table 4.

Single-cell multi-omics sequencing for protein profiling together with their specific applications, results and data sources.

Method	Data source	Molecular layers	Objective and outcome(s)	Platform(s)
PEA [55]	N/A	Panel of up to 96 RNAs and proteins for individual cells from the same population.	To interrogate cell state and find the corresponding cell functions. For most gene products, only a small portion of the variation of protein levels could be explained by measuring mRNA levels in single cells.	the Fluidigm BioMark HD System
REAP-seq [56]	GSE100501	mRNA expression level coupled with 82 antibodies among single cells.	To identify drug response and describe the unknown cell type.	Illumina HiSeq 2500 and 10X Genomics
CITE-seq [57]	GSE100866	Cellular proteins and transcriptomes for thousands of single cells.	To combine highly multiplexed protein marker detection with unbiased transcriptome profiling for thousands of single cells. Multimodal data analysis could achieve a more detailed characterization of cellular phenotypes than transcriptome measurements alone.	Illumina HiSeq 2500
Morita et al. [58]	GSE156934	DNA mutation and cell-surface immunophenotype at the single-cell level in 26 AML patients.	To unravel clonal diversity and evolution patterns of AML. Systematic investigation of predictive and prognostic impact of clonal diversity in AML was possible.	Illumina Human Omni 2.5 BeadChip (hg19) and Mission Bio Tapestri Analysis Pipeline
DBiT-seq [38]	GSE137986	mRNAs, proteins and spatial information in a formaldehyde-fixed tissue slide.	To dissect the initiation of early organogenesis at the whole embryo scale. Deterministic barcoding in tissue enabled NGS-based spatial multi-omics mapping.	Illumina HiSeq 4000 (Mus musculus)
ASAP-seq [59]	GSE156478	Chromatin accessibility and protein levels in single cells.	To decipher the underlying regulatory mechanisms at their respective genomic loci.	NextSeq 550
Miles et al.[60]	dbGAP (phs002049.v1.p1)	Protein expression and mutational information in 17 samples from patients with AML.	To find the correlation of somatic genotype and clonal architecture with immunophenotype. Multiple overlapping immunophenotypic states occurred across samples with divergent genotypes; no community was exclusive to an individual sample.	Illumina NovaSeq and Mission Bio Tapestri Insights