[Arabidopsis] Re: Arab-gen Digest, Vol 89, Issue 2

Prakash M G via arab-gen%40net.bio.net (by pmgnair from gmail.com)
Tue Sep 4 23:31:32 EST 2012


Hello all,

I am looking for some arabidopsis (columbia) wild type seeds.  If anyone
could send me some seeds please reply to my email; pmgnair from gmail.com

Thank you
M.G.Prakash
Konkuk University
Korea

On Wed, Sep 5, 2012 at 2:04 AM, <arab-gen-request from oat.bio.indiana.edu>wrote:

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> Today's Topics:
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>    1. PowerPoint and PDF slides available, Re: [Arabidopsis] LFY
>       ChIP-Seq  data set in Integrated Genome Browser (Loraine, Ann)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 3 Sep 2012 18:26:06 +0000
> From: "Loraine, Ann" <Ann.Loraine from uncc.edu>
> Subject: PowerPoint and PDF slides available, Re: [Arabidopsis] LFY
>         ChIP-Seq        data set in Integrated Genome Browser
> To: "arab-gen from magpie.bio.indiana.edu"
>         <arab-gen from magpie.bio.indiana.edu>
> Message-ID: <CC6A699A.2EF76%aloraine from uncc.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> Hello,
>
> It looks like the image I attached did not go through.
>
> So I've posted a PowerPoint and PDF file with slides showing LFY binding
> sites near the genes mentioned in the iPlant tutorial - AGAMOUS, APETALAl,
> LMI3, etc.
>
> See: http://igbquickload.org/quickload/A_thaliana_Jun_2009/LFYChIPSeq
>
> If you are planning to teach a lecture on ChIP-Seq or if you just want to
> see what the data look like following processing, these may be useful to
> you.
>
> If you have any questions or suggestions please let me know or post to
> this list.
>
> Main "take-home" messages (which may seem fairly obvious) are that the LFY
> IP samples have higher coverage (more reads) than the control and also
> that high-confidence binding sites sometimes occur within large introns in
> the target genes. This has of course been known for some time but it's
> neat to "see" it in a visualization tool.
>
> Lastly, if there are ChIP-Seq data sets you would like to have access to,
> please let me know. Thanks to the resources at iPlant and to open source
> analysis tools, it is now fairly straightforward to make these data sets
> available. And hopefully we can make the processing pipelines more
> accessible through simple, easy-to-follow protocols so that if you are
> using ChIP-Seq techniques in your lab, the bioinformatics data analysis
> will be less of a bottleneck.
>
> Very best wishes,
>
> Ann
>
> -------------------------------
> Ann Loraine, Ph.D.
> Associate Professor
> Department of Bioinformatics and Genomics
> University of North Carolina at Charlotte
> North Carolina Research Campus
> 600 Laureate Way
> Kannapolis, NC 28081
> 704-250-5750
> aloraine from uncc.edu
> http://www.transvar.org
> http://www.bioviz.org
> http://www.uncc.edu
>
>
>
>
>
> On 9/1/12 1:51 PM, "Ann Loraine" <aloraine from gmail.com> wrote:
>
> >Greetings all,
> >
> >The ChIP-Seq data set from Moyroud, et al
> >(http://www.plantcell.org/content/23/4/1293.full) is now available for
> >visualization in Integrated Genome Browser, available from
> >http://bioviz.org/igb.
> >
> >If you are considering using ChIP-Seq to detect transcription factor
> >binding sites, this could be a good data set for you and your students
> >to explore.
> >
> >About the data processing steps:
> >
> >Data were downloaded from Short Read Archive and processed using a
> >protocol adapted from iPlant Tutorial "Using iPlant Discovery
> >Environment and Atmosphere for Advanced ChIP-Seq analysis." (iPlant
> >tutorial is here: https://pods.iplantcollaborative.org/wiki/x/WBK)
> >
> >For more information on the data processing steps or to download data
> >files, see
> >http://igbquickload.org/quickload/A_thaliana_Jun_2009/LFYChIPSeq/.
> >
> >To view the data in IGB, download and launch the IGB from
> >bioviz.org/igb and open the ChIP-Seq data set folder under the Data
> >Access tab.
> >
> >The Data set containing significantly bound regions (p value 0) is
> >named "LFY Filtered Summits."
> >
> >Load the data by clicking the checkbox labeled "LFY Filtered Summits"
> >and change its Load Mode to "Whole Genome" to load all the regions.
> >
> >To view read coverage graphs from the LFY IP and Control, choose data
> >sets named "LFY IP, coverage" and "Control, coverage" and click the
> >"Load Data button." To compare graphs, click the Graph Adjuster tab
> >and adjust the scales so that both graphs are shown in the same scale.
> >
> >An example image from IGB showing coverage graphs and a significant
> >binding site near LFY known target APETALA is attached.
> >
> >Best wishes,
> >
> >Ann Loraine
> >UNCC Bioinformatics and Genomics
> >www.transvar.org
> >www.bioviz.org
> >wiki.transvar.org
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