LFY ChIP-Seq data set in Integrated Genome Browser

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LFY ChIP-Seq data set in Integrated Genome Browser

Ann Loraine
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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PowerPoint and PDF slides available, Re: LFY ChIP-Seq data set in Integrated Genome Browser

Loraine, Ann
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
[hidden email]
http://www.transvar.org
http://www.bioviz.org
http://www.uncc.edu





On 9/1/12 1:51 PM, "Ann Loraine" <[hidden email]> 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
>_______________________________________________
>Arab-gen mailing list
>[hidden email]
>http://www.bio.net/biomail/listinfo/arab-gen


_______________________________________________
Arab-gen mailing list
[hidden email]
http://www.bio.net/biomail/listinfo/arab-gen