Table 1.

A description of the key parameters and applications of various scRNA-seq methods.

Method	Technology Name	Minimum Cells	Developer Company	Advantages	Disadvantages	Cost	Library Preparation Time	Sequencing Depth	Applications	Platforms for Analysis
Droplet-based	Drop-seq	1000	Macosko Lab	High throughput, low cost per cell, UMI-based quantification	Low coverage, limited information on isoforms, SNPs and VDJ rearrangements, cell doublets may occur	USD 0.06–0.2 per cell	1–2 days	0.1–0.5 million reads per cell	Cell type identification, gene expression profiling, trajectory inference	Seurat, Monocle, Scanpy
	inDrop	1000	Klein Lab and Shalek Lab	High throughput, low cost per cell, UMI-based quantification, flexible barcode design	Low coverage, limited information on isoforms, SNPs and VDJ rearrangements, cell doublets may occur	USD 0.06–0.2 per cell	1–2 days	0.1–0.5 million reads per cell	Cell type identification, gene expression profiling, trajectory inference	Seurat, Monocle, Scanpy
	Chromium 10×	500–10,000	10× Genomics	High throughput, low cost per cell, UMI-based quantification, multiple applications (e.g., immune profiling, spatial transcriptomics)	Low coverage, limited information on isoforms, SNPs and VDJ rearrangements, cell doublets may occur	USD 0.55–1.1 per cell	1–2 days	0.5–2 million reads per cell	Cell type identification, gene expression profiling, trajectory inference, immune repertoire analysis, spatial transcriptomics	Cell Ranger, Seurat, Monocle, Scanpy
Full-length	Smart-seq2 (SS2)	1–96	Picelli Lab and Sandberg Lab	High coverage, detection of isoforms, SNPs and VDJ rearrangements, low technical noise	Low throughput, high cost per cell, no UMI-based quantification	USD 35–70 per cell	2–3 days	5–20 million reads per cell	Isoform detection and quantification, SNP calling and phasing, VDJ rearrangement analysis	Cufflinks, DESeq2, edgeR
	Smart-seq3 (SS3)	1–96	Sandberg Lab and Linnarsson Lab	High coverage, detection of isoforms, SNPs and VDJ rearrangements, low technical noise, UMI-based quantification	Low throughput, high cost per cell, requires fine-tuning to balance internal and UMI-containing reads	USD 35–70 per cell (estimated)	2–3 days	5–20 million reads per cell	Isoform detection and quantification, SNP calling and phasing, VDJ rearrangement analysis	Cufflinks, DESeq2, edgeR
	FLASH-seq (FS)	1–96	Picelli Lab	High coverage, detection of isoforms, SNPs and VDJ rearrangements, low technical noise, UMI-based quantification with reduced strand-invasion artifacts, fast and simple protocol	Low throughput, high cost per cell	USD 35–70 per cell (estimated)	<4.5 h	5–20 million reads per cell	Isoform detection and quantification, SNP calling and phasing, VDJ rearrangement analysis	Cufflinks, DESeq2, edgeR

Terms: SNPs: Single-Nucleotide Polymorphisms; UMI: Unique Molecular Identifier; VDJ: rearrangement analysis, analyzing gene rearrangements in immune cells.