Skip to main content

Advertisement

Table 1 Summary of single-cell RNA-seq technologies

From: Single-cell sequencing in stem cell biology

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 [6, 7]
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 [9, 10]
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 [16, 17]
FISSEQ In situ RNA sequencing Rolling circle amplification Full-length mRNAs No 100–1000 No [24]
  1. FACS fluorescence-activated cell sorting, FISSEQ fluorescence in situ sequencing, FRISCR fixed and recovered intact single-cell RNA, MALBAC multiple annealing and looping-based amplification cycles, MARS massively parallel single-cell RNA-sequencing, PCR polymerase chain reaction, PMA Phi29-mRNA amplification, sc single-cell, seq sequence, SMA semirandom primed PCR-based mRNA transciptome amplification, STRT-seq single-cell tagged reverse transcription, TIVA transcriptome in vivo analysis, UMI unique molecular identifier