Table 3.

Methods for transcriptomic analysis of single cells

Method	Platform	Number of Cells (typical)	Description	UMI	Applications	Typical number of sequencing reads per cell
Smart‐seq/Smart‐seq246	Microwell plate/tubes/Fluidigm C1 platform	100s–1000s	Template‐switching PCR‐based full‐length transcript amplification. Can be applied to cells or nuclei (scNuc‐seq)	No	Transcript enumeration Analysis of alternative splicing allelic expression	500 000–4 000 000
CEL‐Seq/CEL‐Seq2 44	Microwell plate/tubes	100s–1000s	In vitro transcription‐based 3′ transcript amplification	Yes	Transcript quantification	100 000–1 000 000
STRT 45, 52	Microwell plate/tubes (also modified for ICell8 Nanogrid52	100s–1000s	Template‐switching PCR‐based full‐length transcript amplification followed by 5′ selection	Yes	Transcript quantification	100 000–1 000 000
sci‐RNA 13	Combinatorial indexing	1000s–10 000s	Combinatorial indexing approach in which transcripts are first indexed during first strand synthesis and subsequently during PCR of 3′ sequencing tags	Yes	Transcript quantification	20 000–200 000
Droplet‐based approaches	Microfluidic platforms: Drop‐seq49 InDrops48 Commercial Platforms: 10X Genomics Chromium Dolomite Nadia	1000s–10 000s	Cells are partitioned into individual droplets and cDNA molecules are uniquely barcoded during reverse transcription	Yes	Transcript quantification	20 000–200 000
Nanowell approaches	Custom Nanowell Chip SeqWell51 Commercial Platforms: Nanogrid (ICell8) BD Rhapsody	1000s–10 000s	Cells are partitioned into individual wells of a custom built nanowell chip and cDNA molecules are uniquely barcoded during reverse transcription	Yes	Transcript quantification	20 000–200 000