Table 1 Summary of single-cell RNA-seq technologies
Assays | Cell capture strategies | cDNA amplification strategies | Target RNAs | Poly(A) minus RNA detection | Number of cells | UMI | Reference(s) |
|---|---|---|---|---|---|---|---|
scRNA-seq | Mouth pipette or FACS | Polyadenylation followed by PCR | Full-length mRNAs | No | 1–100 | No | [5] |
Quartz-seq | Mouth pipette or FACS | Polyadenylation followed by PCR | Full-length mRNAs | No | 1–100 | No | [11] |
Smart-seq/Smart-seq2 | Mouth pipette or FACS | Template-switch followed by PCR | Full-length mRNAs | No | 1–100 | No | |
MALBAC-RNA | Mouth pipette or FACS | MALBAC | Full-length mRNAs | No | 1–100 | No | [12] |
PMA | Mouth pipette or FACS | Rolling circle amplification | Full-length mRNAs | No | 1–100 | No | [13] |
SMA | Mouth pipette or FACS | Semi-random priming followed by PCR | Full-length mRNAs | No | 1–100 | No | [13] |
SUPeR-seq | Mouth pipette or FACS | Random priming followed by PCR | Full-length mRNAs | Yes | 1–100 | No | [32] |
Fluidigm C1 | Microfluidic system | Template-switch followed by PCR | Full-length mRNAs | No | 100–1000 | No | [18] |
Microfluidic scRNA-seq | Microfluidic system | Polyadenylation followed by PCR | Full-length mRNAs | No | 100–1000 | No | [19] |
STRT-seq | Mouth pipette or FACS | Template-switch followed by PCR | 5′ end of mRNAs | No | 10–100 | Yes | |
CEL-seq | Mouth pipette or FACS | In vitro transcription | 3′ end of mRNAs | No | 10–100 | Yes | [8] |
MARS-seq | Robotics and automation | CEL-seq | 3′ end of mRNAs | No | 100–1000 | Yes | [20] |
CytoSeq | Bead-based | CEL-seq | 3′ end of mRNAs | No | >1000 | Yes | [21] |
Drop-seq | Droplet- and bead-based | Template-switch followed by PCR | 3′ end of mRNAs | No | >1000 | Yes | [22] |
inDrop | Droplet- and bead-based | CEL-seq | 3′ end of mRNAs | No | >1000 | Yes | [23] |
TIVA | In vivo mRNA capture based on photo-activation | In vitro transcription | Full-length mRNAs | No | 10–100 | No | [14] |
FRISCR | FACS or fixed cells | SMART-seq2 | Full-length mRNAs | No | 10–100 | No | [15] |
Patch-seq | Aspiration through patch-clamp pipette | STRT-seq/SMART-seq2 | 5′ end of mRNAs or full-length mRNAs | No | 10–100 | Yes/no | |
FISSEQ | In situ RNA sequencing | Rolling circle amplification | Full-length mRNAs | No | 100–1000 | No | [24] |