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Old 05-12-2011, 01:09 PM   #1
aperera
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Default Illumina ChIP-Seq

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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Old 05-13-2011, 01:11 PM   #2
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I don't have an answer for you but I'm also interested in multiplexing ChIP-seq libraries. I was going to try the Tru-seq kit. What kind of problems are you running into?
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Old 05-13-2011, 03:06 PM   #3
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Bioo NEXTflex kits comes with indexed adapters.
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Old 05-17-2011, 06:44 PM   #4
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We're using their indexed adapters for ChIP-Seq, mRNA-Seq and Genomic sequencing. Heard from our sales rep that they are launching a 48 plex ChIP-Seq kit this month

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Bioo NEXTflex kits comes with indexed adapters.
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Old 05-24-2011, 11:37 AM   #5
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We are seeing inconsistent quality of libraries when TruSeq kits are used. I am looking in to Bioo Scientific kits. Also heard that they will release ChIP-Seq kits next. Can not wait!!!
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Old 05-25-2011, 01:42 PM   #6
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NuGen is releasing a low input Chip-Seq kit next month.
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Old 06-13-2011, 10:20 AM   #7
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Has anyone tried the Millipore's Magna ChIP-Seq kit? We are planning on trying this soon and will share results when available.
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Old 06-19-2011, 05:28 AM   #8
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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.
http://www.ncbi.nlm.nih.gov/pubmed/19159457
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Old 06-22-2011, 12:18 PM   #9
Arabette
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Quote:
Originally Posted by aperera View Post
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!
At least you got some success to some extent! I'm about to try this tomorrow (I cannot wait more): I am going to use the TruSeq library prep kit for DNA and change the enzyme and reaction volumes to match the older, validated ChIP protocol and titrate the adapter to account for the much lower amont of material going into the library...is that what you did? Thanks in advance for your reply (possibly by tomorrow!)
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Old 09-28-2011, 09:57 AM   #10
aperera
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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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Old 12-14-2011, 08:02 AM   #11
frigo
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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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Old 12-15-2011, 01:15 AM   #12
ETHANol
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http://seqanswers.com/forums/showthread.php?t=13093

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.
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Old 12-15-2011, 02:19 AM   #13
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Thank you very much for your answer ETHANol !
yes this will be my first shot so I think I'll test the Bioo kit. In a second time I will maybe study your protocol if it can optimized the manipulation.
thank you
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Old 12-16-2011, 07:05 AM   #14
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We are using the Bioo ChIP Seq Kit and have gotten great sequencing results with both Chip DNA and regular genomic DNA. What is truly great is that we can finally multiplex our Chip samples...ahhhhh.
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