Is it important to avoid the peripheral wells for qPCR?
Our qPCR machine is only 96w, not 384w, so losing all the peripheral wells is extremely inconvenient, but of course I'd rather not undermine the quality of my data.
Our qPCR machine is Bio-Rad with LEDs, so they say edge effect isn't as much of an issue:
"Bio-Rad real-time PCR detection systems utilize solid-state optical technology with long-lasting light-emitting diodes (LEDs) for fluorescence excitation and photodiodes for detection. At every position and on every scan, the optics shuttle is reproducibly centered above each well, so the light path is always identical for all wells. "
Is that true? Or should I still avoid the peripheral wells?
Hello
I did use bot BioRad CFX96 and 384 as well as ABI7300, Ependorf Mastercycler and ... . Sometimes I had difficulties with ABI7300 for using peripheral wells but never for BioRad machines. Although I recommend to use white plates only.
Good luck
In my experience, machines that require a passive reference dye are most likely to have problems, due to the single light source and the age of the blocks. We have a CFX96 and always use all of the wells without problems. I agree with Ali, the white plates are the best.
- You are probably fine
- However to be sure, there should be calibrator control plates you can buy to look at sensitivity and S:N for each well
- It is never a bad idea to have these to periodically to check your machine ( 2 x per year)
- Engineers who service your machine will use these plates and if your machine has recently passed a service, then yes you will be fine with all wells
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