Jump to content

  • Log in with Facebook Log in with Twitter Log in with Windows Live Log In with Google      Sign In   
  • Create Account

Submit your paper to J Biol Methods today!
Photo
- - - - -

ChIP DNA sonication problem


  • Please log in to reply
3 replies to this topic

#1 kawaka

kawaka

    member

  • Active Members
  • Pip
  • 20 posts
0
Neutral

Posted 07 March 2005 - 11:13 AM

Hi All,

I am optimizing my ChIP sonication settings. After sonication, I did a reverse crosslink, recovered DNA by phenol extraction and ethanol precipitation. Strangely, most settings gave me a smear around 1 kb and a distinct band at 50 bp. What I expected is a smear between 200-1 kb. Should I ignore the 50 bp band?

#2 methylnick

methylnick

    Veteran

  • Global Moderators
  • PipPipPipPipPipPipPipPipPipPip
  • 245 posts
3
Neutral

Posted 07 March 2005 - 02:34 PM

Strangely, most settings gave me a smear around 1 kb and a distinct band at 50 bp. What I expected is a smear between 200-1 kb. Should I ignore the 50 bp band?

Hi kawaka,

I was wondering what percentage gel you are using, if it is a high percentage I suspect the band you are seeing at 50bp is tRNA or RNA contamination, I think with RNAse this band will dissappear.

Cheers

Nick :D

#3 kawaka

kawaka

    member

  • Active Members
  • Pip
  • 20 posts
0
Neutral

Posted 07 March 2005 - 03:33 PM

Hi Nick, Thank you.

I used 2% gel mistakenly. I never thought of RNA showing up, which I think, makes sense.

K

#4 methylnick

methylnick

    Veteran

  • Global Moderators
  • PipPipPipPipPipPipPipPipPipPip
  • 245 posts
3
Neutral

Posted 07 March 2005 - 04:46 PM

I used 2% gel mistakenly. I never thought of RNA showing up, which I think, makes sense.

no problemo kawaka

Nick :D




Home - About - Terms of Service - Privacy - Contact Us

©1999-2013 Protocol Online, All rights reserved.