Embryonic brains are very delicate and challenging to collect. Still, it is possible, and there are protocols to perform that successfully (a general protocol is attached). I have several general suggestions. For qPCR experiments do not use Phenobarbital or other drugs including isoflurane, because it influences the mRNA levels. Euthanize a female mouse by cervical dislocation.

Do not dissect out immediately the embryo brains, since it is fragile and easily damageable. It is much safer to decapitate and collect the entire heads and work with them under the microscope or a lens to sample the tissue.