Special Question to KPDE - Fast chIP (Feb/26/2007 )

Hi KPDE,

What do you think about my sonication products which have been treated with your fast chIP protocol?

Is the sonication good or not?

Thanks in advance.

-vvmice-

My photo!!

QUOTE (vvmice @ Feb 26 2007, 01:37 PM)

Hi KPDE,

What do you think about my sonication products which have been treated with your fast chIP protocol?

Is the sonication good or not?

Thanks in advance.

-vvmice-

QUOTE (vvmice @ Feb 26 2007, 04:39 AM)

My photo!!

QUOTE (vvmice @ Feb 26 2007, 01:37 PM)

Hi KPDE,

What do you think about my sonication products which have been treated with your fast chIP protocol?

Is the sonication good or not?

Thanks in advance.

I'll just guess on what I see in your gel. The darkest (brightest) smudge at the bottom of the lane is probably RNA and the smear that goes from top to bottom of the lane is probably DNA. The darker part of the smear towards the bottom (but above the RNA), I'm guessing, is the majority of your DNA. If the darkest band at the bottom of your ladder is about 500bp (did I guess right) then the majority of your DNA is in the 250-300bp range, right? It doesn't really get any better than that. You could try to get rid of some of the high molecular weight smear but I doubt that that stuff gets precipitated very efficiently so I don't think it's a problem. Keep in mind, however, that if you are using PCR to analyse your ChIPed DNA then your amplicon size should fit within the average size of your sheared DNA fragments.

-KPDE-