What kits are people currently using to make Illumina multiplexed ChIP-Seq libraries? We are not able to get an answer from Illumina regarding when the TruSeq ChIP-Seq kits will be available or what suggestions they have in the meantime. We have tried using both TruSeq genomic kits and RNA-Seq kits with some luck. However, we are unable to get good libraries consistently. Any feedback/suggestions would be greatly apprecicated!
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Follow the Illumina ChiP-seq protocol, but buy the enzymes from NEB and the primers from IDT (or whoever you buy your oligos from) HPLC or PAGE purified.
See this thread for the primer sequences. http://seqanswers.com/forums/showthread.php?t=198
Just be careful one of the .pdf files that someone posts has a mistake in it. You can also get the primer sequences if you e-mail Illumina but just remember to phosphothiorylate as described in the Illumina thread.
For barcoding/multiplexing ChIP-seq, just add a barcode to the end of the primers as described in this article. And so as you would before.
We designed a multiplex short-read DNA sequencing method to perform efficient ChIP-Seq in yeast and other small genome model organisms. This method produces accurate results with higher throughput and reduced cost. Given constant improvements in high-throughput sequencing technologies, increasing mu …--------------
Ethan
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Originally posted by aperera View PostWhat kits are people currently using to make Illumina multiplexed ChIP-Seq libraries? We are not able to get an answer from Illumina regarding when the TruSeq ChIP-Seq kits will be available or what suggestions they have in the meantime. We have tried using both TruSeq genomic kits and RNA-Seq kits with some luck. However, we are unable to get good libraries consistently. Any feedback/suggestions would be greatly apprecicated!
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Just a quick update...
We tried the Millipore Magna ChIP-Seq kit with the Bioo Scientific adapters, and obtained beautiful libraries. We have only constructed 10 libraries so far, and hope to generate more data points in the near future. Cost per library comes to about $50.
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Hello,
I have to do a ChIP-Seq multiplexed library and I would like to have some feedback about using the Truseq library prep kit and the Bioo Scientific kits. Does someone tries these kits ?? Is there too much problems with the Truseq library prep kit?
About the Millipore's Magna ChIP-Seq kit, it's use to do a ChIP and a sequencing but I just have to do the sequencing from ChIP samples. Does someone knows other kits ?
Sorry for my bad english and thank you for your answers
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Any non-primary sequence heritable modification of genetic material. ChIP-SEQ, DNA methylation (Bisulfite-SEQ), chromatin modifications (methylation, acetylation, etc), non coding RNA.
I'd say go with the Bioo kit as it is essentially what I am doing. The TruSeq kit you will have to modify some, and if this is your first shot, perhaps you don't want to be working out your own modifications. But I would also consider using my protocol in the linked in the thread above as the Kapa polymerase is significantly more efficient then Phusion (side by side comparison in hands) and Phusion is significantly better then the TruSeq polymerase at least according to the advertising.--------------
Ethan
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