Table 1.

Summary of important scRNA-seq technologies and platforms

Technology	Year	Single-cell isolation	Gene coverage	Library amplification	Throughput	Advantages	Disadvantages	References
10x- Genomics	2017	Droplet	3′ or 5′	PCR	Very high (> 10,000)	High throughput; identifies cells well; ease of use; high cell flux; short library construction cycle; ultra-high capture efficiency	Many steps for DNA library construction; high sample requirements; specialized experimental equipment; non full-length information	[35]
CEL-seq	2012	Micromanipulation	3′	In vitro transcription	Low (1–200)	High specificity and accuracy; first method to use IVT for the amplification	Low efficiency; reduced sensitivity for low expression transcripts	[31]
CEL-seq2	2016	FACS	3′	In vitro transcription	Low (1–200)	High sensitivity; low cost; low hands-on input	Strong 3′ preference; high-abundance transcripts are preferentially amplified	[32]
Cyto-seq	2015	Microwell platform	3′	PCR	High (1000–10000)	Direct analysis of complex samples	Expensive and time-consuming	[233]
Drop-seq	2015	Droplet	3′	PCR	High (1000–10000)	High throughput; low cost; fast amplification; equipment is easily obtained	Low mRNA capture efficiency and low sensitivity	[33]
FLASH-seq	2022	FACS	Full length	PCR	High (1000–10000)	Increased sensitivity and reduced hands-on time compared to Smart-seq3	High manual technical requirements	[62]
inDrop	2015	Droplet	3′	In vitro transcription	High (1000–10000)	High throughput; low cost; strong cell capture capabilities; simplified process	Extremely low cell capture efficiency	[34]
MARS-seq	2014	FACS	3′	In vitro transcription	Median	Reduced amplification bias and labeling errors; high reproducibility	High manual technical requirement	[41]
MARS-seq2	2019	FACS	3′	In vitro transcription	High (1000–10000)	Greatly reduced background noise compared with MARS-seq; minimizes sampling bias and simplifies steps	High manual technical requirement	[44]
MATQ-seq	2017	Micromanipulation	Full length	PCR	Low (100–200)	High sensitivity and accuracy; high transcript capture rate	Inefficient cell lysis	[30, 234]
Microwell-seq	2018	FACS	3′	PCR	High (1000–10000)	High throughput; low cost; high sequencing quality	Presence of 3′ bias; FACS requires skilled operators	[52]
Microwell-seq2	2020	FACS	3′	PCR	High (1000–10000)	Higher utilization of micropores and higher throughput than Microwell-seq; high sensitivity and stability	Presence of 3′ bias; FACS requires skilled operators	[53]
Quartz-seq	2013	FACS	Full length	PCR	Low (1–200)	High sensitivity and high reproducibility	High manual technical requirements	[26]
Quartz-seq2	2018	Droplet	Full length	PCR	High (1000–10000)	High sensitivity; high reproducibility; high accuracy	High manual technical requirements	[36]
SCAN-seq	2020	Dilution	Full length	PCR	Low (1–200)	High sensitivity and accuracy	Low throughput; high cost; high error rate of Nanopore sequencing,	[65]
SCAN-seq2	2023	FACS	Full length	PCR	High (1000–10000)	High throughput and sensitivity; much cheaper than SCAN-seq	Relatively more expensive and lower throughput compared with drop-based scRNA-seq	[66]
sci-Plex	2019	In situ barcoding	3′	PCR	Very high (> 10,000)	Massively multiplex platform; cost-effective; high throughput for drug screening; high resolution	Low UMIs per cell; low cell recovery rate,	[57, 235]
Sci-RNA-seq	2017	In situ barcoding	3′	PCR	Very high (> 10,000)	Minimized perturbation of RNA integrity	Some cell types cannot be defined	[54]
Sci-RNA-seq3	2019	In situ barcoding	3′	PCR	Very high (> 10,000)	Higher throughput; lower cost; nuclei are extracted directly from fresh tissues without enzymatic treatment	Tn5 transposome loaded with specific oligos is not commercially available; reduced gene detection rate compared with 10 × Genomics	[56, 236]
Seq-Well	2017	Microwell platform	3′	PCR	High (1000–10000)	Easy-to-use; portable; low-cost; efficient cell lysis and transcriptome capture	Low cell capture efficiency	[48]
Seq-Well S3	2020	Microwell platform	3′	PCR	Very high (> 10,000)	High-throughput; high-fidelity	Short cDNA; presence of 3 'bias	[50]
SMART-seq	2012	FACS	Full length	PCR	Low (1–200)	Full-length coverage	Low efficiency; limited throughput and read coverage	[27]
SMART-seq2	2013	FACS	Full length	PCR	Median (100–1000)	Higher sensitivity and higher transcription coverage; cell capture visualization; low amplification bias; low variability and low noise; analysis of rare cell populations	No early multiplexing; low reproducibility; extremely high manual technical requirements	[28]
SMART-seq3	2020	FACS	Full length	PCR	Median (100–1000)	Much more sensitive and higher throughput than SMART-seq2; provides cost-effective RNA analysis at isoform resolution	No early multiplexing; extremely high manual technical requirements	[59]
Smart-seq3xpress	2022	FACS	Full length	PCR	High (1000–10000)	Shortens and streamlines the Smart-seq3 protocol to substantially reduce reagent use and increase cellular throughput	No early multiplexing; extremely high manual technical requirements	[60]
SPLit-seq	2018	In situ barcoding	3′	PCR	Very high (> 10,000)	Low cost and minimal equipment requirements; no need for cell isolation; suitable for fixed cells and fixed nuclei	Not enough genes	[55]
STRT-seq	2011	FACS	5′	PCR	Median (100–1000)	Multiplexable; can be used to study many different single cells at a time; reduced cross-contamination	PCR biases; nonlinear PCR amplification	[37]
VASA-seq	2022	Plate-based formats and droplet microfluidics	Full length	PCR	High (1000–10000)	The only single-cell sequencing technology that combines high sensitivity, full-length transcriptome coverage; with high throughput; cost-effective; compatible with all sample types	Integration with other datasets (which necessitates batch corrections), and creation of specialized data analysis pipelines	[67, 68]