Any opinions on the best real time instrument for multiplexing? Currently have Cepheid's smartcycler 1 and looking into upgrading to smartcycler 2 or ABI 7500 or 7900. Is Stratagene's instrument any good for multiplexing?

Thanks in adavance.

Stratagene's Mx3000 is great. I've used one for the past year and half, and it's way better than anything I've worked on before, like the iCycler, ABI instruments, and MJR cyclers.

You can check Rotor-Gene (Corbett Reserch) for real-time PCR. They have even 6 channels so you can amplify 5 target genes and 1 control together in one tube. Some modifications of Rotor-Gene have HRM function (high resolution melting) which could be applied for detection mutation, for instance.

ccisotope:

One thing you might want to evaluate before making the purchase is the software that comes with the real time thermocyclers. In my experience this is something that I overlooked and regret that I did. Make sure the software does not demand large setup times for each run and that it exports data in a format that easy to handle.

One important criterion is the choice of primer-probe design software that comes as a package with these instruments. Stratagene MX 300 and 4000 instruments bundle the industry standard Beacon Designer software. ABI bundles PrimerExpress while Bio-Rad again finds Beacon Designer as the instrument of choice for real time pcr assay design.