ChIP sample storage - DNA Methylation, Histone and Chromatin Study

ChIP sample storage - (Mar/17/2008 )

Hi there,
I'm about to start some bulk ChIP experiments using various antibodies. For small scale ChIP, I used to store pellets of fixed cells at -80C. Considering that I want to use different antibodies on the same samples (preferably sonicated under exactly the same conditions), I was wondering if there's a possibility to store the supernatant after sonication (fixation in 0.5-1% formaldehyde) for longer time periods (1-2 weeks) prior to IP ... Does anyone by any chance know if this is possible without loosing quality of the prep?
Thanks & Cheers,
Jan

-jhb80-

Hi Jan,

It just so happens that we did an experiment to answer this question just last week! When we do a ChIP we only use ~6 million cells/IP, so sometimes we have heaps of chromatin left over (after cross-linking, lysis, sonicating and pre-clearing). We have frozen this chromatin and then repeated the same ChIP ~2 weeks later. We got *exactly* the same results as the first time we performed the ChIP
Hope this helps
Clare

QUOTE (jhb80 @ Mar 17 2008, 02:29 PM)

-Clare-

Hi Clare,
Now that's perfect timing
Helps a lot, thank you very much for the info!
Cheers,
Jan

-jhb80-

QUOTE (jhb80 @ Mar 17 2008, 01:08 PM)

Hi Clare,
Now that's perfect timing

Helps a lot, thank you very much for the info!
Cheers,
Jan

I've always aliquoted my chromatin out with very small aliquots because I have found that, while freezing the sonicated chromatin once does not significantly decrease the yield, freezing and thawing a second time can decrease the signal for some factors (particularly those that are hard to pull down, like TFs and kinases). If you are only looking at histones and histone modifications then you can probably freeze and thaw a few times without any problems.

-KPDE-

QUOTE (jhb80 @ Mar 17 2008, 08:08 PM)

Hi Clare,
Now that's perfect timing

Helps a lot, thank you very much for the info!
Cheers,
Jan

No worries

-Clare-