Single prokaryotic cell isolation and total transcript amplification protocol for transcriptomic analysis

Nat Protoc. 2015 Jul;10(7):974-84. doi: 10.1038/nprot.2015.058. Epub 2015 Jun 4.


Until recently, transcriptome analyses of single cells have been confined to eukaryotes. The information obtained from single-cell transcripts can provide detailed insight into spatiotemporal gene expression, and it could be even more valuable if expanded to prokaryotic cells. Transcriptome analysis of single prokaryotic cells is a recently developed and powerful tool. Here we describe a procedure that allows amplification of the total transcript of a single prokaryotic cell for in-depth analysis. This is performed by using a laser-capture microdissection instrument for single-cell isolation, followed by reverse transcription via Moloney murine leukemia virus, degradation of chromosomal DNA with McrBC and DpnI restriction enzymes, single-stranded cDNA (ss-cDNA) ligation using T4 polynucleotide kinase and CircLigase, and polymerization of ss-cDNA to double-stranded cDNA (ds-cDNA) by Φ29 polymerase. This procedure takes ∼5 d, and sufficient amounts of ds-cDNA can be obtained from single-cell RNA template for further microarray analysis.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Bacteria / genetics
  • Bacteria / isolation & purification
  • Cell Separation / methods
  • DNA, Bacterial / genetics
  • DNA, Bacterial / isolation & purification
  • DNA, Complementary / genetics
  • DNA, Complementary / isolation & purification
  • Gene Expression Profiling / methods*
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Laser Capture Microdissection / methods
  • Prokaryotic Cells / cytology*
  • Prokaryotic Cells / metabolism*


  • DNA, Bacterial
  • DNA, Complementary