Applications of single-cell sequencing in cancer research: progress and perspectives

Lei, Yalan; Tang, Rong; Xu, Jin; Wang, Wei; Zhang, Bo; Liu, Jiang; Yu, Xianjun; Shi, Si

doi:10.1186/s13045-021-01105-2

Journal of Hematology & Oncology

Table 1 Summary of important single-cell sequencing technologies and platforms

From: Applications of single-cell sequencing in cancer research: progress and perspectives

Measurement	Technology	Platform	Year	Single cell isolation	Gene coverage	Barcode addition	Library amplification	Reaction volume	Throughput	References
Transcriptome	SPLit-seq	Plated-based, Illumina NextSeq	2018	Not needed	3′	Ligation of barcoded RT primers	PCR	Microliter	High	[8]
	SCI-RNA-seq	Plate-based, Illumina NextSeq 500	2017	Not needed	3′	Barcoded RT primers	PCR	Not needed	High	[17]
	Seq-well	10X Genomics, Illumina NextSeq 500	2017	Droplet	3′	Barcoded RT primers	PCR	Nanoliter	High	[191]
	inDrop	Not mentioned	2015	Droplet	3′	Barcoded RT primers	In vitro transcription	Microliter	High	[192]
	Drop-seq	10X Genomics, Illumina NextSeq 500	2015	Droplet	3′	Barcoded RT primers	PCR	Nanoliter	High	[193]
	Microwell-Seq	Plate-based, Illumina HiSeq	2018	FACS	3′	Barcoded RT primers	PCR	Microliter	High	[18]
	MARS-seq	Plate-based	2014	FACS	3′	Barcoded RT primers	In vitro transcription	Microliter	High	[194]
	CEL-seq 2	Fluidigm C1, illumine TrueSeq	2016	FACS	3′	Barcoded RT primers	In vitro transcription	Microliter	Low	[195]
	SMART-Seq 2	Plate-based, Illumina HiSeq 2000	2013	FACS	Full length	Library PCR with barcoded primers	PCR	Microliter	Low	[196]
Genomics	TARGET-seq	Plate-based, Illumina NextSeq 500/550	2019	FACS	3′ and full-length	Barcoded RT primers	PCR	Microliter	High	[53]
Epigenomics	CoBATCH	10X Genomics; Illumina HiSeq X	2019	FACS	Full length	Barcoded PAT transposase	PCR	Microliter	High	[197]
Epigenomics	scATAC-seq	10X Genomics, Illumina NextSeq 500	2013	FACS	full length	Barcoded primers	PCR	Microliter	High	[198]
Transcriptomics, proteomics	CITE-seq	10X Genomics, Illumina HiSeq 2500	2017	Droplet	3′	Barcoded RT primers	PCR	Nanoliter	High	[199]
	REAP-seq	10X Genomics, Illumina HiSeq 2500	2017	FACS	3′	Barcoded RT primers, DNA-barcoded antibodies	PCR	Microliter	High	[200]
	INs-seq	10X Genomics, Illumina NextSeq 500	2020	FACS	5′	Barcoded RT primers	In vitro transcription	Microliter	High	[66]

RT: reverse transcription; SPLiT-seq: split-pool ligation-based transcriptome sequencing; SCI-Seq: single-cell combinatorial indexed sequencing; FACS: fluorescence-activated cell sorting; MARS-seq: massively parallel single-cell RNA sequencing; inDrop: indexing drop RNA sequencing; ScATAC-seq: single-cell transposase-accessible chromatin using sequencing; CoBATCH: combinatorial barcoding and targeted chromatin release; PAT: Tn5 transposase to protein A; CITE-seq: cellular indexing of transcriptomes and epitopes by sequencing; REAP-seq: RNA expression and protein sequencing assay; INs-seq: intracellular staining and sequencing

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