ChIP-on-chip hybridization troubleshooting - any good websites? (Mar/11/2008 )

Hi,

I am having trouble with my hyb step for chip-on-chip. Are there any good websites out there with good info on what can go wrong, and how to fix it etc?
I had a look but couldn't find anything useful.

The problem I had with my second hyb was that the distribution of up (and down) regulated regions were not random. There was a circle! A student tried to tell me it was because my sample was too hot (not possible) and an expert told me it was due to our whole hyb system (Agilent gasket slides etc).

Thanksn advance!
Clare

here are a couple of websites and some literature from agilent:

microarray station

guide to microarray data analysis

it sounds as though you had a bubble trapped in the sandwich. this happened to me once. it looked like a hole in the array (right in the center).