problems with CHEF

[amalkova]

My lab needs help with CHEF gels (separation of entire chromosomes). We are having constant problems with CHEF for the last two years. Before that, we never had problems for 6 years. We have Bio-RAD DRII system. The problem is that chromosomes look like double-bands or just having a smear above the main band. (So it cannot be degradation). During these two years the machine was sent twice to Bio-RAD. Both times they replaced many parts. After coming back, it was working O’K for about a month, and then will go back to this double-band pattern. Moreover, the last time this machine was being repaired, we had a loaner – a brand-new CHEF Mapper. It was great at the beginning, but started giving us double bands later. We started washing the machine overnight with warm water. It helped a little bit, but still the problem came back. We changed sources of water. Sometimes helped a little bit, but did not eliminate the problem. We tried to run a diluted bleach trough the system. We also noticed that this problem doesn’t depend on any particular plug preparation. When the problem starts, it works the same for everybody. We simply ran out of ideas and BIO-RAD has no idea as well. We would really appreciate some help.