I'm currently performing a DNase-seq study on some plant material but do not have access to PFGE machinery. As I understand it the PFGE is required to separate the HMW DNA, so that one can be sure that digestion has occurred throughout accessible regions of the genome.To try and circumvent the use of PFGE I have more or less followed the protocol as laid out by Cumbie et al. 2015 in which they use standard electrophoresis. My problem is however that the authors provide no guidance as to which digestion pattern on a standard gel is ideal for DNase-seq.
So, id PFGE only important for identifying the ideal digestion or is there also another reason? Can I identify the ideal digestion pattern using standard gel electrophoresis?
In my point of view, PFGE is used also to separate large fragments of DNA
You can substitute a regular agarose gel for the short end of the PFGE range. If you set it to 30 volts and run overnight, you can get pretty decent resolution up to ~50 kb. Use a long tray if you have one, otherwise you'll lose the shorter bands.
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