Slide hybridization/washing problem - (Apr/09/2008 )
Dear all,
recently performed my first ChIP-chip but the slides don't look good at all 
Any suggestions what could have gone wrong?
Cheers
Kylvalda
Hi Kylvalda,
Can you post a close up of the spots? What was the data like after you used Feature Extraction (or whatever program?).
You do have a kind a halo effect happening which is most likely a hybridisation issue. Can I ask what hyb system and slides you are using? We are also trying to get chip-chip working nicely (almost there! so close!). And we're in Cambridge too 
We are using the scanner at IMS.
Clare
Can you post a close up of the spots? What was the data like after you used Feature Extraction (or whatever program?).
You do have a kind a halo effect happening which is most likely a hybridisation issue. Can I ask what hyb system and slides you are using? We are also trying to get chip-chip working nicely (almost there! so close!). And we're in Cambridge too
We are using the scanner at IMS.Clare
Hi Clare,
haven't prcessed the data yet (gonna do this this weekend...).
Am using Agilent slides, hybing chambers, oven and gaskets together with selfmade hybridization and wash buffers.
Hmm, if your surname begins with P and you got two-coloured hair then we already met (how are the Nanog primers by the way?
Closeup of spots will be posted at the weekend after first trials with feature extractor....
Cheers
Kylvalda
Hi Clare,
haven't prcessed the data yet (gonna do this this weekend...).
Am using Agilent slides, hybing chambers, oven and gaskets together with selfmade hybridization and wash buffers.
Hmm, if your surname begins with P and you got two-coloured hair then we already met (how are the Nanog primers by the way?
Closeup of spots will be posted at the weekend after first trials with feature extractor....
Cheers
Kylvalda
[/quote]
Hi hi,
Yep, we know eachother! The nanog primers were not good :/ But that's ok, we're going to do a hyb with the anti-H3K27 and see how that goes.
Your slides look exactly like our second hybs did. We didn't go on to analyse them because there was a distinct pattern of spots (it's easier if I explain this over a QC report). Anyway, to cut a long storry short, we're probably not going to use the Agilent system anymore...and only use Feature Extraction to obtain raw data. We are using a SlideBooster which only requires a 16h incubation for our hybs and we'll attempt to analyse using R with the Ringo package. We'll be over at IMS scanning tomorrow if you want to meet up and chat?
Clare