Hello,
I am interested in running an experiment requiring pulsed field electrophoresis. The primary samples will be budding yeasts chromosomes and minor set of samples with chromosome sizes up to 5.7MB. Looking at the literature and current market instruments, it seems Biorad instruments are the most popular and with the majority of the protocols optimized for the older generation ( Bio Rad CHEF-DR III). I would be happy if someone with technical experience in running this kind of experiment or in pulsed field electrophoresis in general would provide feedback on choice of instrument for example would you go for CHEF-DR III variable angle system (I am leaning towards this one) or the newer CHEF Mapper® XA system or is there other alternatives?
additionally any tricks the to reduce running cost would be great, for example:
1- Can you run old DRII cells with newer systems or can you run the DRIII cell with the Mapper system?
2- Have you had success casting the agarose gel for the system using non standard parts (meaning parts other than provided by biorad)?
P.S I do realize that sequencing should resolve most issues that PFGE can, however, I would like to run few samples with this.
Getting the latest model is better because you will have better service from biorad if anything goes wrong. To reduce running costs make sure to not leave it standing idle for long because this is when you run into blockages in the tubes From sedimentation of the running buffer. If it’s running a lot make sure you give it a wash with 37c deionised water to clear it before it goes idle. Keep the lid open when it’s idle. be very careful when cleaning the wires as they are very expensive to replace. good Luck
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