Method for analyzing RNA

A method of analyzing a sample comprising at least two different RNA species, each having a sequence comprising a target sequence that is a distinctive protein coding sequence and a distinctive PCR tag in a 3′ untranslated region (UTR), said at least two different RNA species prepared by RNA in vitro transcription, the method comprising determining the presence, integrity and/or quantity of each of the RNA species present in said sample using RT-qPCR that comprises the following steps:

• a) contacting said sample with at least one primer for reverse transcription under conditions sufficient for reverse transcription, thereby providing a sample containing cDNA;
• b) contacting the sample containing cDNA with different sets of PCR primers under conditions sufficient for PCR amplification of the cDNA, wherein each set of PCR primers includes one primer capable of binding to the distinctive PCR tag of the cDNA corresponding to one RNA species within the sample, but not to the cDNA corresponding to other RNA species within the sample, thereby producing amplified DNA corresponding to the at least two different RNA species;
• and
• c) quantifying the amplified DNA corresponding to the at least two different RNA species,
• wherein said at least two different RNA species are at least 200 nucleotides in length and:
• (1) have a length that is no more than 10% different from one another;
• and (2) 3′ UTR sequences that are at least 80% identical to one another.