Our lab has been noticing that whenever we hybridize BAC probes on FISH slides, there is a lot of background/debris that is very visible under DAPI. This is problematic to a point that it is sometimes hard to see the signals.

As you can see from the pictures attached, even from the same slide, the area that hybridized with BAC probe, there is a lot of background seen under DAPI filter. But, the area that didn’t come in contact with BAC probe, it has a clean background.