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Old 06-06-2012, 12:48 PM   #1
menzies
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Default Multiplexing RNA-Seq and ChIP-Seq in same lane

Is it OK to multiplex RNA-Seq and ChIP-Seq samples into the same lane? My ChIP is sheared to around 300bp using sonication, and the RNA-Seq samples are fragmented to 300-400bp by cationic RNA fragmentation.

The only problem I can think of is the effect of different-sized fragments on qPCR library estimation (before mixing to multiplex the samples). Are there any other problems I haven't thought of?
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Old 07-24-2012, 08:31 AM   #2
UKboston
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I just asked Illumina tech support about this:
In general, multiplexing ChIP-Seq libraries is possible but not supported since it is difficult due to low input material levels, high number of PCR cycles necessary, and inefficiency of the three-primer multiplex PCR. For TruSeq Cluster Kits it is not possible to do multiplexing of ChIP-Seq with Small RNA v1.0, v1.5. Please find this informaiton also on website: http://support.illumina.com/sequenci...atibility.ilmn
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Old 07-26-2012, 07:50 PM   #3
luckylove
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Quote:
Originally Posted by UKboston View Post
I just asked Illumina tech support about this:
In general, multiplexing ChIP-Seq libraries is possible but not supported since it is difficult due to low input material levels, high number of PCR cycles necessary, and inefficiency of the three-primer multiplex PCR. For TruSeq Cluster Kits it is not possible to do multiplexing of ChIP-Seq with Small RNA v1.0, v1.5. Please find this informaiton also on website: http://support.illumina.com/sequenci...atibility.ilmn
do you mean that chip-seq samples should be sequencing alone in one lane. and in this lane the best thing is there is no other kind of sequencing samples? thank you!
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Old 07-27-2012, 08:00 AM   #4
UKboston
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That's what it sounds like to me, though the reasons are unclear to me. I read elsewhere that, while not recommended, it is possible to multiplex ChIP-seq libraries. I haven't done it and have no immediate plans to do so.

Last edited by UKboston; 08-06-2012 at 09:03 AM.
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