Hi,
we are going to purchase the AriaMx qPCR system from agilent. One of the reasons we choose this system is the possibility to add filters cartridge later to upgrade the system. Thus, we would like to choose 2 cartridge to start. However, the representative propose the Sybr/FAM and ROX filters. Since I have poor experience in multiplex experiments, can you help me to choose among the filters proposed (SYBR/FAM; HEX; ROX; CY3; CY5; ATTO425). The idea is to have the possibility to run duplex experiments.
Thanks
We have two of those instruments, with 4 and 5 filters. In most cases, when multiplexing, we are using FAM and HEX combination. If you need second filter only for reference dye, then use FAM and ROX combination.
Note that probes that are labeled with FAM are the cheapest. HEX labeled probes are more expensive than FAM but significantly cheaper than probes labeled with ROX, CY5 and CY3. So, if you are using 2 probes, FAM and HEX combination will be much cheaper then FAM and ROX, FAM and CY5 or FAM and CY3 combination.
Best regards
The answer from Dejan is very thorough and detailed. In addition, we use TET a lot for multiplexing and works very well in combination with FAM. If it is an option, I highly recommend a filter that will work with TET.
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