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I often find the term "RT-PCR" used in articles without any further qualification. Searching for the meaning of the acronym sometimes leads to "real-time polymerase chain reaction" and sometimes "reverse transcription polymerase chain reaction." I understand that reverse transcription PCR uses a reverse transcriptase to convert RNA to DNA, which is then amplified by the usual PCR method. I'm not sure I understand what real-time PCR is, but it sounds to be distinct from reverse transcription PCR. Are these distinct methods that happen to have the same abbreviation? Or do they somehow mean the same thing? What is usually meant by the acronym "RT-PCR"? Is there some context I can use to distinguish them?

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    $\begingroup$ Related: biology.stackexchange.com/questions/95268/… $\endgroup$ – Bryan Krause Sep 23 at 22:02
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    $\begingroup$ Does this answer your question? RT-PCR: Not seeing how it can measure mRNA expression levels $\endgroup$ – Alex Reynolds Sep 23 at 23:06
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    $\begingroup$ Unfortunately, there is no real and hard definition and it can mean both, depending on the context. $\endgroup$ – Chris Sep 24 at 4:49
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    $\begingroup$ Real-time PCR is used to quantify a target in real time, thus is sometimes called quantitative PCR (qPCR). Basically, any mention of Ct or Cq values indicates a real-time PCR methodology. If they are quantifying a DNA target, it's likely referring to real-time PCR (aka qPCR). If they are using it to detect (not quantify) a target from RNA, it's probably reverse-transcription PCR. If they are quantifying an RNA target (like gene expression from mRNA), it's likely RT-qPCR (real time reverse transcription PCR). $\endgroup$ – MikeyC Sep 24 at 14:33
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    $\begingroup$ @MikeyC That was the answer I was looking for: it that states the definitions in a systematic and unambiguous way. If it were an answer and not a comment, I would accept it. $\endgroup$ – WaterMolecule Sep 24 at 15:08
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Real-time PCR is used to quantify a PCR target by measuring some indicator of target amplification in real time after each amplification cycle, thus it is sometimes(often) called quantitative PCR (qPCR). The key to distinguishing between reverse transcription PCR and real-time PCR in the context of a paper or protocol is to look at the starting material being used and the data output.

If the source material is RNA, it needs to be reverse-transcribed into cDNA before PCR amplification. And if they're showing quantification of a specific target, it's likely a real-time PCR of some sort. Quantification of a gene target from normal DNA is likely a standard real-time PCR (aka qPCR). Quantification of an RNA target (like gene expression from mRNA), is likely quantitative reverse transcription PCR (RT-qPCR). The same goes for if the starting material is cDNA (end product of an RNA reverse transcription reaction). Lastly, any mention of Ct or Cq values (or delta-Ct, or delta-delta-Ct) generally indicates a real-time quantitative methodology.

If they are citing the use of RT-PCR to simply confirm the presence or absence of a target (sometimes called endpoint PCR) or to amplify it for downstream applications like sequencing, with no mention of specific target quantification, it's likely a standard reverse-transcription PCR.

There are exceptions to some of these rules, but it should help get you through most literature with some idea of what methods are being used.

Edit: In the past few days, I've seen multiple papers using "RT-PCR" as shorthand (I guess) when they were talking about RT-qPCR or rRT-PCR. Like I said, always exceptions to the rule. But as long as you read the methods it should be simple enough to figure out.

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  • $\begingroup$ Why was this downvoted? Is it incorrect? $\endgroup$ – WaterMolecule Sep 25 at 16:49
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    $\begingroup$ An addition: real time PCR or qPCR requires a a dye which binds to dsDNA. This will give you readings of RFU (relative fluorescence units) per Cycle. In RT-qPCR the dye binds to the dsDNA from the conversion of ssRNA by RT. $\endgroup$ – m4rio Sep 29 at 20:49

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