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CHIP enrichment varies? anyone can help? - (Feb/04/2008 )

When I did CHIP, I did exactly same procedure and I got similar pattern of results. but the enrichment changes every time. ie. i've got enrichment of my p1 protein at 15 fold at highest and 5 fold enrichment at lowest. so i wonder what affect this enrichment? how should I do to keep at high enrichment?


Thanks a lot. blush.gif

-cathyli-

QUOTE (cathyli @ Feb 4 2008, 01:42 PM)
When I did CHIP, I did exactly same procedure and I got similar pattern of results. but the enrichment changes every time. ie. i've got enrichment of my p1 protein at 15 fold at highest and 5 fold enrichment at lowest. so i wonder what affect this enrichment? how should I do to keep at high enrichment?


Thanks a lot. blush.gif


How are you calculating enrichment?

-KPDE-

QUOTE (KPDE @ Feb 4 2008, 07:58 PM)
QUOTE (cathyli @ Feb 4 2008, 01:42 PM)
When I did CHIP, I did exactly same procedure and I got similar pattern of results. but the enrichment changes every time. ie. i've got enrichment of my p1 protein at 15 fold at highest and 5 fold enrichment at lowest. so i wonder what affect this enrichment? how should I do to keep at high enrichment?


Thanks a lot. blush.gif


How are you calculating enrichment?

ddCt method (ddct=(Ctinput-Cttarget gene)-(Cinput- Ctno bind gene)
then calculate fold enrichment power(ddCt,2)

-cathy-

QUOTE (cathy @ Feb 6 2008, 04:37 AM)
QUOTE (KPDE @ Feb 4 2008, 07:58 PM)
QUOTE (cathyli @ Feb 4 2008, 01:42 PM)
When I did CHIP, I did exactly same procedure and I got similar pattern of results. but the enrichment changes every time. ie. i've got enrichment of my p1 protein at 15 fold at highest and 5 fold enrichment at lowest. so i wonder what affect this enrichment? how should I do to keep at high enrichment?


Thanks a lot. blush.gif


How are you calculating enrichment?

ddCt method (ddct=(Ctinput-Cttarget gene)-(Cinput- Ctno bind gene)
then calculate fold enrichment power(ddCt,2)


One thing that will affect your enrichment is the amount of chromatin used (if you are anywhere near saturating your antibody then more chromatin will result in less enrichment). I usually try to adjust the input for each experriment that so I'm using the same amount of chromatin.

-KPDE-