Can I multiplex my assays if my amplicons are not all the same length?
Yes, it is possible. The amplicons do not have to be the same length in order to duplex the assays. You need to use different reporter dyes on the probes in multiplex - they should have a substantial difference in maximum emission wavelength to be effective. A classic example is to use FAM and VIC for the 2 probes. Depending on the expression of the targets, you may also need to limit the primer concentration for one of the assays. This is common when duplexing a target and endogenous control (the control probe is VIC labeled and the primer concentration is decreased so the target assay can properly compete for use of enzyme and dNTPs).
Can I check the end product of a TaqMan Gene Expression Assay by running an agarose gel?
Yes, you can check the end product on an agarose gel. If you use the TaqMan Universal PCR Master Mix (including AmpErase UNG, Cat. No. 4304437), we recommend running the gel immediately after the PCR, since the trace amount of AmpErase UNG may digest the end product that contains double-stranded DNA with dUTP incorporated. The average length of amplicon ranges from 50-150 bp. The exact amplicon length is indicated on the detailed page of each assay on our website. You can get to that page by clicking on the Assay ID; the amplicon information is listed in the section "Assay Details".
Can I set up and store the TaqMan Fast Universal PCR Master Mix at room temperature if the instrument is in use?
For optimal results, we recommend to run the reaction plate right after setting up the reaction. If a reaction plate cannot be run within 2 hours of completing the reaction setup, then freeze/refrigerate the reaction plate until it can be loaded and run on the fast PCR instrument platform.
Can I run a reaction made with the standard TaqMan Universal PCR Master Mix in fast thermal cycling mode?
No, we do not recommend this approach. Since the standard TaqMan Universal PCR Master Mix is not optimized for running with fast thermal cycling, assay results will be significantly compromised.
Can I compare performance of assays between the TaqMan Fast Universal PCR Master Mix compare and TaqMan Universal PCR Master Mix?
In general, assays have been found to perform comparably with these reagents, but they may not provide exactly identical results.