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comparisons with NGS dat? Re: [Arabidopsis] Re: good set of"housekeeping" genes in AT?

comparisons with NGS dat? Re: [Arabidopsis] Re: good set of"housekeeping" genes in AT? - Arabidopsis and Plant Biology

comparisons with NGS dat? Re: [Arabidopsis] Re: good set of"housekeeping" genes in AT? - Discuss Arabidopsis and Plant Biology Research.


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Old 10-05-2009, 12:42 PM
Ann Loraine
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Default comparisons with NGS dat? Re: [Arabidopsis] Re: good set of"housekeeping" genes in AT?



Thank you for this excellent advice!

I've been following this thread with great interest in hopes of finding good
controls for expression experiments.

Has anyone assessed the behavior of "invariant" (in quotes because they may
still vary under some treatments) genes using next-gen sequencing data?

There are a several new Illumina data sets available in the short-read
archive (from Oregon State) and my lab has a data set from a 454 sequencing
experiment (longer reads) comparing a treatment and control.

We were thinking of using the "invariant" genes to calculate a normalization
factor across the data sets so that we could more confidently estimate
differential expression, and then, of course, follow up with another gene
measurement method (e.g., qRT-PCR) to confirm the results.

Knowing which genes really do not vary (much) under our conditions of
interest will be critical.

Best,

Ann Loraine

On Sat, Oct 3, 2009 at 7:30 PM, Eve Wurtele <[Only registered users see links. ]> wrote:

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