Dear all,
I have to do some CHIP QPCRs to check the Histone acetylation. I am not familiar with the primer design on the promoter region. As far as I know, primer design is a crucial part on the CHIP QPCR. Could any one please help me on primer design?
Gene-rat ROCK1
Accession no-NM 031098.1
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CHIP primers
Started by Raviraj, May 12 2009 09:23 PM
6 replies to this topic
#1
Posted 12 May 2009 - 09:23 PM
#2
Posted 13 May 2009 - 03:08 AM
Here you go.
A 500 bp promoter sequence (very CpG rich)
A 500 bp promoter sequence (very CpG rich)
AAAATGGGAGAGTGAGCCTGTTCTGTGGAAACCAGCTCTTGGCCGAGGATAAATCAGTGC GTCTTACCGGGCCGAGTGGAACCCGGGATGCAGGGCTAGACAGCCGCTAGCGCCTTAGAG CGGAGCGGGGCCGGCCCGGGGCCCAGGCGGCAGCTGGCGCAGCTCCTCACCCGCCCTTCG CTTTCGCCTTTCCTCTTCGCCCTCCCTGGCTGCCCCGAGGGAGTCTCCACCCTGCTGCGC TCCCTCTTCCCGCCGCTGCCCTTCTCTGGACTGGGCCCCGCCATGGCGAAGGCAGCCGGG GCCCGCTAGGCTGAGGTGCCTCGCCGGAGCGACCGGGCTGCTGGCGACGGCGCTGTCGGC TGTCGCGAGGGGCTGCCGGGTGGGATGCGACTTTGGGTGTCCGAGCGGCTGCGGGTCGCT GTCACCCCCAGCCTGGGGTCTAGAGAGCAGAGGTCCCCTCAGTGAGGGGAAGGAGGGGGA ACCGGGCGCACCTGGTGACCTwo sets of ChIP primers on the promoter:
LEFT PRIMER 5 20 59.99 55.00 3.00 1.00 11.00 TGGGAGAGTGAGCCTGTTCT RIGHT PRIMER 104 19 60.93 63.16 4.00 2.00 10.00 GCTGTCTAGCCCTGCATCC PRODUCT SIZE: 100 LEFT PRIMER 378 18 62.49 61.11 4.00 0.00 9.00 GGGTGGGATGCGACTTTG RIGHT PRIMER 477 18 60.60 66.67 3.00 3.00 11.00 CCCTCCTTCCCCTCACTG PRODUCT SIZE: 100Hope that works
#3
Posted 13 May 2009 - 05:30 PM
Thanks a lot pcrman

#4
Posted 19 May 2009 - 09:53 AM
Hi Pcrman,
What software did you use for designing these primers?
Thanks
Mura
What software did you use for designing these primers?
Thanks
Mura
Here you go.
A 500 bp promoter sequence (very CpG rich)AAAATGGGAGAGTGAGCCTGTTCTGTGGAAACCAGCTCTTGGCCGAGGATAAATCAGTGC GTCTTACCGGGCCGAGTGGAACCCGGGATGCAGGGCTAGACAGCCGCTAGCGCCTTAGAG CGGAGCGGGGCCGGCCCGGGGCCCAGGCGGCAGCTGGCGCAGCTCCTCACCCGCCCTTCG CTTTCGCCTTTCCTCTTCGCCCTCCCTGGCTGCCCCGAGGGAGTCTCCACCCTGCTGCGC TCCCTCTTCCCGCCGCTGCCCTTCTCTGGACTGGGCCCCGCCATGGCGAAGGCAGCCGGG GCCCGCTAGGCTGAGGTGCCTCGCCGGAGCGACCGGGCTGCTGGCGACGGCGCTGTCGGC TGTCGCGAGGGGCTGCCGGGTGGGATGCGACTTTGGGTGTCCGAGCGGCTGCGGGTCGCT GTCACCCCCAGCCTGGGGTCTAGAGAGCAGAGGTCCCCTCAGTGAGGGGAAGGAGGGGGA ACCGGGCGCACCTGGTGACCTwo sets of ChIP primers on the promoter:LEFT PRIMER 5 20 59.99 55.00 3.00 1.00 11.00 TGGGAGAGTGAGCCTGTTCT RIGHT PRIMER 104 19 60.93 63.16 4.00 2.00 10.00 GCTGTCTAGCCCTGCATCC PRODUCT SIZE: 100 LEFT PRIMER 378 18 62.49 61.11 4.00 0.00 9.00 GGGTGGGATGCGACTTTG RIGHT PRIMER 477 18 60.60 66.67 3.00 3.00 11.00 CCCTCCTTCCCCTCACTG PRODUCT SIZE: 100Hope that works
Edited by mura, 19 May 2009 - 09:57 AM.
#5
Posted 19 May 2009 - 12:09 PM
The primers were designed using Primer3. You can use any program to design ChIP primers. The important thing is that you need to decide which region of your gene you want to examine.
#6
Posted 27 July 2009 - 02:01 AM
Hi pcrman, how do i determine which region is the promoter sequence from the sequence I obtained from fasta format?
#7
Posted 27 July 2009 - 06:07 AM
would you please let us know how did you determine the promoter region. and can i use Primer Express from ABI to generate CHIP primers?
There is one databse in the following link. Is this good?
http://rulai.cshl.ed...=searchPromForm
Thanks
There is one databse in the following link. Is this good?
http://rulai.cshl.ed...=searchPromForm
Thanks
Here you go.
A 500 bp promoter sequence (very CpG rich)AAAATGGGAGAGTGAGCCTGTTCTGTGGAAACCAGCTCTTGGCCGAGGATAAATCAGTGC GTCTTACCGGGCCGAGTGGAACCCGGGATGCAGGGCTAGACAGCCGCTAGCGCCTTAGAG CGGAGCGGGGCCGGCCCGGGGCCCAGGCGGCAGCTGGCGCAGCTCCTCACCCGCCCTTCG CTTTCGCCTTTCCTCTTCGCCCTCCCTGGCTGCCCCGAGGGAGTCTCCACCCTGCTGCGC TCCCTCTTCCCGCCGCTGCCCTTCTCTGGACTGGGCCCCGCCATGGCGAAGGCAGCCGGG GCCCGCTAGGCTGAGGTGCCTCGCCGGAGCGACCGGGCTGCTGGCGACGGCGCTGTCGGC TGTCGCGAGGGGCTGCCGGGTGGGATGCGACTTTGGGTGTCCGAGCGGCTGCGGGTCGCT GTCACCCCCAGCCTGGGGTCTAGAGAGCAGAGGTCCCCTCAGTGAGGGGAAGGAGGGGGA ACCGGGCGCACCTGGTGACCTwo sets of ChIP primers on the promoter:LEFT PRIMER 5 20 59.99 55.00 3.00 1.00 11.00 TGGGAGAGTGAGCCTGTTCT RIGHT PRIMER 104 19 60.93 63.16 4.00 2.00 10.00 GCTGTCTAGCCCTGCATCC PRODUCT SIZE: 100 LEFT PRIMER 378 18 62.49 61.11 4.00 0.00 9.00 GGGTGGGATGCGACTTTG RIGHT PRIMER 477 18 60.60 66.67 3.00 3.00 11.00 CCCTCCTTCCCCTCACTG PRODUCT SIZE: 100Hope that works