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cpgware primer design, does it work


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4 replies to this topic

#1 mstefani

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Posted 10 January 2005 - 05:53 AM

Hi,
Im trying to design a primer set for two genes which go true methylation analysis. I chose upstream UTR plus upstream region (1000bp upstream) from the gene. Is it ok?
Has anybody used cpgware primer design software? Does it work or should I use some other software? Im in a bit hurry, so I would appreciate if somebody could help me!

-Karoliina

#2 pcrman

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Posted 10 January 2005 - 09:53 AM

Hi Karoliina,

I would suggest that you first identify CpG islands within the promoter of your genes and then design primers on those regions.

I have not tried CpGware yet because it is not freely accessible.

Check out this post to find the necessary tools for your purpose.
http://www.protocol-...?showtopic=4589

#3 folkman

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Posted 01 March 2005 - 05:43 PM

Hi,
I'm a new one in epigenetic. Now, I 'm trying to design a primer for MSP, I want to know whether the PCR product should contain all CpG island region? or I should design all CpG island primer of the gene's promoter for analysis the status of mythlation?
thanks

#4 pcrman

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Posted 01 March 2005 - 07:54 PM

Hi Folkman,

Yes, methylation analysis should foucs on CpG island region that surrounding the promoter. If you'r gonna do MSP, design your primer on some important CpG sites. What is in the product doesn't matter because MSP can only detect methylation status of CpG sites within the primer. The product size should be around 100-200 bp but doesn't necessarily need to contain the whole CpG island.

Good luck!

#5 folkman

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Posted 06 March 2005 - 05:04 PM

pcrman, I just wanted to say thanks to you.

all the best




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