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Old 06-01-2015, 07:06 AM   #1
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Location: Upstate NY

Join Date: Feb 2013
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Default Opinions/Experiences with targeted RNA-Seq?

I recently had a people ask me about possible options for cheaper sequencing for when there are pre-defined genes of interest, and I started to look into targeted RNA-Seq, specifically from Illumina since our core facility has a MiSeq and it would be great for that. We sometimes order TLDA PCR arrays for validation, but that is relatively expensive for larger numbers of samples. With the targeted system, we could pick 100-ish genes and then just multiplex to run all samples in one lane, in which case the library kit/probe order would be the most expensive part.

I saw a couple of threads on here about targeted RNA-Seq but not many responses. Does anyone have any experience or opinions on it compared to running RT-qPCR on TLDAs or OpenArrays? Is it less expensive (through Illumina) than TLDAs for 10-20 samples and 50 - 100 genes?

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illumina, targeted rna-seq

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