I am investigating Glial fibrillary acidic protein (GFAP) expressing cells in the prefrontal cortex of an alcohol (adolescent) mouse model. The right hemisphere of the mouse brain was sectioned coronally at 50 um using a freezing microtome. Alternate sections were processed for Nissl and GFAP with appropriate primary and secondary antibodies, using standard immunohistological procedures.

Upon analysis (unbiased stereological procedures) it appears that the astrocytes are clustered in the area where the corpus callosum starts to form. There are very few to none in the area that is characterized as the prefrontal cortex in the mouse brain.

I have exhausted my search in literature and came up empty. Could it be that there was a problem with the antibody during the immunohistological procedure or maybe a problem with the tissue itself? I have five experimental groups and the findings are the same throughout.

What could the reason for this be?