Whole-brain clearing in 8% SDS

BJ2014BJ2014 Posts: 8
edited March 2015 in Hydrogel Embedding
Has anyone tried clearing a whole mouse brain in 8% SDS after hydrogel embedding? I don't have the resources to do PARS clearing, so I am thinking of putting a perfused brain in hydrogel overnight @ 4degC, followed by 3-4hr incubation @ 37degC water bath. Any thoughts on the plausibility of this?


  • AdamAdam Posts: 31
    I've done this, takes a long time to passively clear though, if that's what you mean.
  • BJ2014BJ2014 Posts: 8
    Yes passively clearing in 37C incubation chamber on a shaker using 8% SDS. So the whole brain does eventually clear?
  • AdamAdam Posts: 31
    It does, but takes a long time (months). Depends on the acrylamide concentration you choose, but hemisections can be cleared much faster if that is appropriate for what you want to do.
  • dgrobertsdgroberts Posts: 16
    A whole mouse brain embedded in standard Hydrogel (4% acrylamide) cleared in 4% SDS took me about 10-12 weeks. I'm now only doing hemispheres, which take less than 2 months under the same conditions.
  • dgrobertsdgroberts Posts: 16
    I would also crank up the temperature to 45 degrees or so in the beginning stages of the clearing process.
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