Hello all,

I am following this protocol for kainic acid-induced seizures in mice:

1. Inject KA i.p. at 12 mg/kg

2. Wait 2 hours, monitoring for seizure-like activity

3. Sacrifice the animal and harvest the brain

By using c-Fos intron and exon FISH probes, I was able to resolve distinct intron signal in the nucleus under a confocal microscope at 25X magnification, but found that the exon signal in the cytoplasm was not visible at all. We've eliminated most factors as the cause, including tissue fixation, the FISH protocol, and the probes/buffer. It seems like the only factor left to consider is the behavioral paradigm. Other groups have managed to get successful resolution of both intron and exon signal, and my hypothesis is that the mRNA may be degraded in the cytoplasm prior to sacrifice, although I have not been able to find any papers that examine this issue in detail. Any advice on the protocol would be greatly appreciated!