Shearing (sonication) problem for ChIP - Using Bioruptor (Jun/10/2009 )

Hi guys,

I was in the forum long time ago and then there was a crisis and now I became a new member. =) Anyway, I have some difficulties shearing my DNA and I cant seem to get the size I want (200 to 500 bp). I am using Bioruptor and the settings are max for 20 cycles (30 sec sonication, 30 sec ice) - means it is 20 minutes.

My cell number is roughly 2.5 x 10^6. But I still cant get the sheared DNA.

Should I really use MNase treatment? or should I reduce my cell number? or should I increase my SDS lysis buffer?

Thanks alot for any input.

cheers.

Welcome back Timjim!

I've never used a bioruptor and could not offer much help. The sonication time required by bioruptor is unusually longer than probe based sonicators. I read the bioruptor protocol and it seems you follow it quite well. The only thing you can do probably is to further increase the cycle. Some cells are just more refractory to sonication.

Hello

We use a Bioruptor too. I am a little concerned that you aren't seeing sheared DNA after 20 minutes!! We cross-link our cells in formaldehyde at a final conc. of 1% for 10 mins. Then we sonicate at approx. 1 million cells per 30ul (as recommended by the company). For us, approx. 7 minutes is fine

What are your cross-linking conditions?

Clare

timjim on Jun 10 2009, 10:24 PM said:

Hi Clare,

Thanks for your input. I am using the same fixation as well for 1% formaldehyde and then glycine to stop the fixation. But I have to admit, probably it is longer than 10 minutes. Maybe 15 or 20 minutes and I read the bioruptor manual and it says that the longer the fixation, the longer is the sonication. So maybe the fixation is the problem here.

pcrman,

Thanks for the welcoming back. I am back finally again.

What is the maximum cycle for sonication? I dont want my DNA to be less than 100bp!

thanks alot guys

Hi again

You're right - increased fixation = increased sonication. Are you doing TF or histone ChIPs?
Clare

timjim on Jun 11 2009, 10:21 AM said:

Hi Clare,

i am doing Histone ChIP. What are the tips for this unique technique? Thanks!

Easy then There's no way to need to fix for 15-20 mins for histones! What cells are you using? I suggest you fix for 10 mins only, then sonicate for 7 mins (high, 30 sec on/off). We use human T cells, neutrophils and myeloid blast cells for our ChIPs and 7 mins is fine. You may want to try 5 mins, 7 and 10 or something. And try the 1 mill cells/30ul and see how you go

Let us know how you get on!

Clare

timjim on Jun 11 2009, 10:53 AM said:

timjim on Jun 11 2009, 02:21 AM said:

Do you use thin walled tubes (like the 0.5ml tubes you would use for PCR) for sonication? We switched to those and the efficiency of sonication increased dramatically. Also, we rigged up a cooling apparatus (a parastaltic pump rigged to copper coil in a bucket of ice water with tubes circulating the water through the bioruptor; it's actually really simple to set up) so that we don't have to use ice in the bioruptor. The ice was severely decreasing our sonication efficiency.

Hi guys, here is my latest shearing.

1 = roughly 1.8 x 10^6
2 = dilution of 2
4 = dilution of 4

20 min is 20 cycles of shearing and likewise 30 min is 30 cycles

I am quite skeptical with the band at the bottom. Are those too much shearing effect? And the shadow effect is due to the loading dye.

What do you guys think? Can I proceed? But I dont like the smearing above 1.5kb.
Thanks!

timjim on Jun 12 2009, 02:19 AM said:

How high above 1.5kb does the smearing go? If it only goes as far as 2kb or so I would proceed. You may not be able to get much better than that. As far as the band at the bottom, I highly doubt that it is due to overshearing as I get that band regardless of how much shearing I do. It's probably RNA fragments or something like that since it is at such a low MW.