Single-Cell Tagged Reverse Transcription Sequencing

STRT-Seq is a method similar to CEL-Seq that involves unique barcoding and sample pooling to overcome the challenges of samples with limited material (Islam et al., 2011) (Islam et al., 2012). In this method, single cells are first picked in individual tubes, where first-strand cDNA synthesis occurs using an oligo(dT) primer with the addition of 3_6 cytosines. A helper oligonucleotide promotes template switching, which introduces the barcode into the cDNA. The barcoded cDNA is amplified by single-primer PCR. Deep sequencing allows for accurate transcriptome determination of individual cells.


  • Barcoding and pooling allows for multiplexing and studying many different single cells at a time
  • Sample handling and the potential for cross-contamination are greatly reduced due to using a single tube per cell


  • PCR biases can underrepresent GC-rich templates
  • Nonlinear PCR amplification can lead to biases affecting reproducibility
  • Amplification errors caused by polymerases will be represented and sequenced incorrectly
  • Loss of accuracy due to PCR bias
  • Targets smaller than 500 bp are amplified preferentially by polymerases during PCR


Illumina Library prep and Array Kit Selector


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