[Arabidopsis] LFY ChIP-Seq data set in Integrated Genome Browser

Ann Loraine via arab-gen%40net.bio.net (by aloraine from gmail.com)
Sat Sep 1 12:51:52 EST 2012


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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