[Arabidopsis] A question about biotin treatment to plant seedlings

Ann Loraine via arab-gen%40net.bio.net (by aloraine from uncc.edu)
Thu Mar 17 19:49:04 EST 2011


My lab has observed a dramatic change in transcript accumulation patterns 3
hours after a heat shock. We also observed dramatic changes in splicing
patterns for some genes.

We haven't tested earlier times points via RNA-Seq, but publicly-available
microarray data sets reveal mRNA abundance differences only 1/2 hour after
comparable treatments.

If you can find a microarray experiment that resembles your experimental
design, I would recommend looking at that first because it can give you an
idea of what to expect.

Very best wishes,

Ann Loraine

On 3/17/11 4:55 PM, "Xi Chen" <cxde from iastate.edu> wrote:

> Sorry for bothering. I want to clarify my question again, due to some
> unclear description in my first e-mail.
> I have a general question about how soon after a mechanical or chemical
>> perturbation Arabidopsis seedlings will have a transcriptional  response
>> detectable by a deep seq method.
>> If you have conducted a dose response experiment to a stimuli using deep
>> seq methods, could you let me know when you began to get a detectable shift
>> in transcript accumulation .
> PS: In my case, I am using biotin as chemical perturbation.
>>  Thank you so much!
> Xi
> On Thu, Mar 17, 2011 at 12:58 PM, Xi Chen <cxde from iastate.edu> wrote:
>> Hello researchers,
>> Sorry to bother you, I have a question about how soon Arabidopsis seedlings
>> will respond to the biotin treatment. For example, I will treat my
>> Arabidopsis seedling samples with biotin starvation for a while, and add
>> biotin into it to see how the transcriptional profile changes. But I don't
>> know how to pick the treatment timing, 30 min or 1 hr. Do you have any
>> suggestion or comments for this. Thank you so much!
>> Best,
>> Xi
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Ann Loraine
Associate Professor
Dept. of Bioinformatics and Genomics, UNCC
North Carolina Research Campus
600 Laureate Way
Kannapolis, NC 28081

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