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Old 05-07-2010, 01:24 AM   #1
Junior Member
Location: Germany

Join Date: Feb 2010
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Default Illumina mRNAseq multiplexing

Hi you all,

we want to start mRNAseq with barcoded / multiplexed libraries on our Illumina GA II. Has anyone ever tried this? The standard Illumina multiplexing kit is designed for genomic DNA. Has anyone also used this for mRNAseq? Any modifications necessary?

Or has anyone tried other approaches to this like using custom primers...

Any help would be great,

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Old 05-08-2010, 07:57 AM   #2
Shawn Baker
Location: San Diego

Join Date: Aug 2008
Posts: 84

Yes, you can definitely run indexed/multiplex libraries of RNA-Seq samples on the GA II (and HiSeq 2000). You just need to substitute multiplex adapters and PCR primers from the multiplexing kit for the adapters that are in the mRNA-Seq kit.

Shawn Baker
Market Manager, Expression and Epigenetics
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Old 05-18-2010, 09:56 AM   #3
Location: London

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Agree with scbaker about hte multiplexing.

We have used indexing by PCR primers for small RNA but I can't see why it wouldn't work for mRNA as you use the small RNA adapters with the strand specific protocol, although will need a bit of work.
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Old 05-31-2010, 10:37 PM   #4
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Default Works


thanks to both of you and sorry for the late reply but we wantet to test your suggestions first.

So the protocol works fine and we have successfully duplexed and triplexed samples using this approach.

Best regards,

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