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Table 1 Comparison of the characteristics and applications of different scRNA-seq technologies

From: Recent developments in application of single-cell RNA sequencing in the tumour immune microenvironment and cancer therapy

Characteristics and applications

Drop-Seq, In-Drop

STRT-seq, SMART-seq2

CEL-seq, MARS-seq

CytoSeq

SPLiT-seq

Microchip

Approaches

Microdroplet approaches

Microwell plate-based approaches

Microwell plate-based approaches

Microwell plate-based approaches

Other approaches

Microfluidics

Single cell separation and capture

Microdroplets

FACS

FACS

FACS

None

Micofluidics

Number of cells in a single run

5000–10,000

50–500

500–2000

100–10,000

> 100,000

48–96

Sensitivities of gene detection

Cell line: 5000 genes per cell

Tissue: 1000–3000 genes per cell

Cell line: 7000–10,000 genes per cell

Tissue: 2000–6000 genes per cell

Cell line: 7000–10,000 genes per cell

Tissue: 2000–6000 genes per cell

Cell line: 7000–10,000 genes per cell

Tissue: 2000–6000 genes per cell

Cell line: 7000–10,000 genes per cell

Tissue: 2000–6000 genes per cell

Cell line: 6000–9000 genes per cell@@@Tissue: 1000–5000 genes per cell

Strength

High throughput;

Low cost;

Easy to operate;

High degree of automation

Flexible optimization;

Low requirements for cell sample size;

Many quality control points;

Full cDNA sequencing;

High sensitivity of gene detection

Low cost;

High throughput;

Conducive to targeted capture

Low cost;

High throughput;

Larger number of samples processed at one time;

High capture rate;

Low requirements for sample preparation

Capture maximum 96 cells in a single run;

Low technical requirements;

Short experiment period;

Full cDNA sequencing;

High sensitivity of gene detection

Weakness

High requirements for cell number and activity;

3’ sequencing instead of full cDNA sequencing;

Lack of quality control points

Manual operation;

High technical requirements;

Low throughput and high cost;

Time consuming

High requirement for cell number;

3’ sequencing instead of full cDNA sequencing;

Complicated procedure

3’ sequencing instead of full cDNA sequencing

Lack of quality control points;

Low throughput;

High costs

Application

Clustering and lineage determination in large-scale cell samples;

Cells with diameter < 40 µm

Experienced researchers;

In-depth analysis of small sample size

Clustering and lineage determination in large-scale cell samples;

Cells with diameter < 20 µm

Clustering and lineage of large-scale cell sample;

In-depth analysis of small sample size

In-depth analysis of small sample size

Cells with diameter of 5–25 μm

Commercial platform

10 × Genomics

BD rhapsody

Fluidigm C1

  1. “–” not applicable. FACS fluorescence-activated cell sorting