I have whole mouse brains fixed in PFA that I need to microdissect specific regions: hippocampus, cerebellum, striatum,and frontal cortex for DNA methylation analysis. Is there a staining (or any other) technique I could use to verify that I have dissected the region I intended, and that there is not contamination with surrounding regions?
There are so many YouTube concerning brain dissection.
I will just put one of them here.
Isolation of adult mouse hippocampus - YouTube
We base our dissections on Mouse brain atlas. However, I don't know if there are any stainings to see contamination during the dissection as such. Normally after dissection, when the tissues are processed for RNA or DNA, you could use a region-specific marker to validate this issue.
Hi Eric, I am not really sure what you meen under "microdissected speific regions".
Just in case you have cut the brain conronally or horizontally on a cryostate or vibratom then you have the possibility to mount, let me say, evera 6th section on a slide. After air drying you can stain the sections with cresylviolett. This so called Nissl-stain helps orientating. If you need the whole block where your structure of interest is in, you have to use the coordinates of the Pxinos-Brain-Atlas. Good luck!
Please have a look at this paper, maybe it's helpful for your question:
Article Gene profiling of laser-microdissected brain regions and sub-regions
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