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. 2013 Jul 31;8(7):e70714. doi: 10.1371/journal.pone.0070714

Figure 2. Comparison of RIN values and qRT-PCR results of different FFPE and cryopreserved samples.

Figure 2

RIN and ct-values generated by qRT-PCR of RNA extracted from 65 different samples of 15 patients are shown. Corresponding aliquots of different tissue types were (A) cryopreserved or (B) fixed in formalin and embedded in paraffin. The majority of cryopreserved samples have RIN values above 5 while the majority of FFPE samples show low RIN values between 2 and 3. 11 FFPE samples showed high RIN values above 3 and up to 8 but ct values of the qRT-PCR assays of these samples were not substantially lower than in the other FFPE samples. In CRYO samples the Pearson correlation factor between RIN and ct values is −0.5 to −0.6, in FFPE samples the correlation factor is −0.25 to −0.28 depending on amplicon length. The difference in ct values obtained from CRYO or FFPE samples is statistically significant (p<0.01). PCR was performed in triplicates and median ct is shown. Samples not amplifying or yielding unspecific products were set to a ct of 40 (but omitted from statistical analysis).