QRT-PCR/Single tube

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This protocol describes one-step real time quantitative reverse transcription PCR to quantify relative levels of a particular mRNA sequence between two samples. This technique is also called known commerically as Taqman, qRT-PCR, real-time PCR. This particular protocol describes use of a flourescent labeled probe (FAM) to provide readings.

Starting Materials

  • Validated PCR primers & probe that are efficient over the range of RNA that you are assaying. Primers are typically designed with a 58 degree Tm but may vary by lab.
  • PCR primers and probe for a house keeping gene (ie B-actin, GAPDH, RPL19)
  • Taq Polymerase, MuLV RT
  • dNTPs, MgCl2, nuclease free water
  • PCR strip caps or 96-well plates with transpearant caps
  • total RNA (~50ng per reaction, diluted to 10ng/ul)

Basic Principle

  • Combine RT, Taq, dNTPs, primers, probe and RNA in a single tube. Add enzymes last.
  • Reverse transcribe the RNA for ~ 30' to form a template for Taq-mediated PCR.
  • Do 40 cycles of PCR. Measure the levels of template after each cycle with a real-time PCR machine.
  • Analyze the results.


  • Generate a 10x solution for each gene target that includes the appropriate forward primer, reverse primer, and labelled probe (FAM-BHQ1, FAM-TAM, etc).
  • Combine RT, Taq, dNTPs, MgCl2 and H20 in a single tube called your master mix. Make sure to add enzymes last. Mix by pipetting (do not vortex enzymes).
  • Add the appropriate quantity (refer to your kit) of master mix to 10x primer mix.
  • Dilute RNA to ~ 10ng/ul. Pipet 5 ul into each well.
  • Add PCR reaction mix for each gene target into the appropriate well.
  • Cycles for MuLV reverse transcriptase with Amplitaq Gold from Applied Biosystems. This program may need adjustments depending on your primer design. It's a good starting point.
    • 30' at 48 degrees
    • 10' at 94 degrees
    • 40 Cycles
      • 30" 94 degrees
      • 60" 60 degrees
      • (optional) 60" 72 degrees
    • END
  • The first time you use a primer set it is a good idea to run the sample out to ensure that you're getting one band, thus showing that your primers are specific for your desired gene product.


Delta-Delta Ct Method. See Livak KJ, Schmittgen. Methods 25 402-408 (2001)

Comments & Tips

  • Use a master mix to ensure a consistent amount of enzyme in each tube that you will be comparing.

Protocol Endorsements