Whole-Transcript Amplification for Single Cells

The Quartz-Seq method optimizes whole-transcript amplification (WTA) of single cells (Sasagawa et al., 2013). In this method, an RT primer with a T7 promoter and PCR target is first added to the extracted mRNA. RT synthesizes first-strand cDNA, after which the RT primer is digested by exonuclease I. Next, a poly(A) tail is added to the 3′ ends of first-strand cDNA, along with a poly(dT) primer containing a PCR target. After second-strand generation, a blocking primer is added to ensure PCR enrichment in sufficient quantity for sequencing. Deep sequencing allows for accurate, high-resolution representation of the whole transcriptome of a single cell.

Similar methods: CEL-Seq, Drop-seq, MARS-Seq, CytoSeq, inDrop, Hi-SCL


  • Single-tube reaction suitable for automation
  • Digestion of RT primers by exonuclease I eliminates amplification of byproducts
  • Short fragments and byproducts are suppressed during enrichment


  • PCR biases can underrepresent GC-rich templates
  • Amplification errors caused by polymerases will be represented and sequenced incorrectly
  • Targets smaller than 500 bp are preferentially amplified by polymerases during PCR


Illumina Library prep and Array Kit Selector


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