I was wondering if anyone has familiarity with embedding fixed rat brain tissue using agar or agarose for sectioning on a vibrating microtome (Vibratome)? My supervisor feels that it might be worthwhile to consider embedding our tissue using these procedures since it might facilitate sectioning on a vibratome.  (We often want to collect sections that could potentially range from 20  to 40 microns depending on experimental procedure).    Would someone be able to provide me with a detail procedure and/or protocol for embedding rat brain tissue?   Also is there a reason for why one should use agar versus agarose for embedding?   And could this embedding procedure potentially interfere with immunostaining?   

I appreciate your help and any suggestions,

Neil
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