[PDF] Real-time RT-PCR (TaqMan™) protocol - Yellow fever virus (YFV)





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PCR les données concernant la quantité du produit amplifié sont enregistrés « en temps réel » La quantification repose sur la phase exponentielle mais exploite un nouveau paramètre : le Ct V Principe du Ct La PCR quantitative en temps réel repose sur un nouveau principe de quantification : On ne regarde plus combien mais quand

Can TaqMan®gene expression assays be used in duplex real-time PCR?

Duplex reactions using TaqMan®Gene Expression Assays Duplex real-time PCR is the simultaneous amplification and measurement of two target sequences in one reaction. TaqMan®Gene Expression Assays can be used in duplex real-time PCR when using a FAM™dye-labeled assay in combination with a primer-limited, VIC®dye-labeled assay.

What should I know before using TaqMan® PCR core reagents kit?

Check the settings of the dye components before data analysis. Decrease in ROX™ dye fluorescence (passive reference dye). Precipitation in the TaqMan® buffers occurs. • When using the TaqMan® PCR Core Reagents Kit, be sure to mix the tubes well. • Use TaqMan® Gene Expression Master Mix (2 ?).

What cDNA template should be used for qPCR?

10 50 cDNA Template (1-100ng)§ § Applied Biosystems recommends that the qPCR reaction not be composed of more than 20% of the reverse transcription reaction. 420 RNAse-free water 4 20 50TaqMan®Gene Expression Assays Protocol

What size amplicon should be used in qPCR reaction?

The size of amplicon in qPCR reaction is between 75-200bp to ensure higher amplification efficiency. For primer and probe design in this purpose, the software Primer Express v2.0 from ABI is highly recommended, especially for TaqMan chemistry, which needs both sequence specific primers and fluorescence labeled probe.

Real-time RT-PCR (TaqMan™) protocol - Yellow fever virus (YFV) Real-time RT-PCR protocol - Yellow fever virus (YFV)

1. Master mix

Component Volume per reaction Volume for 10

reactions

Volume for 50

reactions RNase/DNase-free water 6.4 µl * 64 µl * 320 µl * reaction buffer (2x) 12.5 µl * 125 µl * 625 µl * primer 1 (100 µM) 0.25 µl 2.5 µl 12.5 µl primer 2 (100 µM) 0.25 µl 2.5 µl 12.5 µl probe (25 µM) 0.15 µl 1.5 µl 7.5 µl enzyme 0.5 µl * 5 µl * 25 µl *

Total per reaction 20 µl

2. RNA

Add 5 µl of RNA to 20 µl of master mix.

Include positive and negative controls to evaluate the validity of the run.

3. Cycling conditions

1 cycle:

50C for 30 min * (reverse transcription)

95C for 2 min * (DNA polymerase activation,

45 PCR cycles:

95C for 15 seconds

60C for 1 min

4. Interpretation

positivity: Ct value assay validity: positive and negative controls should show the expected results

5. Primers and probes

The use of the following primers and probes is recommended: Domingo et al., J Clin Microbiol 50, 4054-60 (2012)

YFallF (YF15-38F) 5'-GCTAATTGAGGTGYATTGGTCTGC

YFallP (YF41-64FAM) 5'-FAM-ATCGAGTTGCTAGGCAATAAACAC-BHQ1

YFallR (YF83-103R)

5'-CTGCTAATCGCTCAAMGAACG

or

Johnson et al., CDC (not published)

YF14-34F 5'-TGCTAATTGAGGTGCATTGG

YF34-57FAM 5'-FAM-TCTGCAAATCGAGTTGCTAGGCA-BHQ1

YF115C 5'-CTGGTCAGTTCTCTGCTAATCG

* -Step qRT-PCR Kit (Invitrogen, catalog number: 11732-020 or 11732-088) and should be adjusted when other enzymes are used.

Disclaimer: The mention of specific companies or of certain manufacturers' products does not imply that they are endorsed or

recommended by the Pan American Health Organization in preference to others of a similar nature that are not mentioned.

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