Download QPX methods 117KB Aug 15 2012 08:14:13 PM

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QPX gene ontology in response to heat stress: Questions, Proteins, eXamples
Annie Page-Karjian, Maya Groner, Jamie Sziklay, Ana Elisa Garcia, Ashton
Griffin, Gregor-Fausto Siegmund, Sonia Singhal, Steven Roberts
Keywords:
Abstract
Introduction
QPX, clams,
Temperature (mucus and cell) –hypothesis? We hypothesize that altered
biochemical pathways will be associated with changes in temperature? Specifically
we are interested in virulence factors, mucus production, cell growth and responses
to heat stress. HELP!
Virulence factors and QPX and methods to id
Methods
BLURB about how QPX was grown/ strain, etc.
We used ILUMINA (LOCATION) to create an mRNA sequence library for QPX at each
of the two temperature treatments (10°C and 21°C). This created ~400 million
reads. The resulting libraries were trimmed using XX stringency and a de novo
assembly was performed using both libraries in CLC () (bubble size? And stringency
x?). This resulted in a backbone consisting of 11,271 contigs.
Gene annotation
The contigs from our de novo assembly were annotated by BLASTx against the Swis
Prot database (). The annotation was delimited with a maximum e-value of 10-5 and
limited to a single hit per contig. Gene ontologies and GO SLIM ontologies were
assigned to Swiss Prot accession numbers for the annotated contigs.
Differential Expression
RNA-Seq was performed by comparing contigs from each library against the de novo
backbone using CLC bio (??). Genes with more than a 2-fold difference in expression
were were annotated using the previously annotated backbone. Enrichment
analyses were performed in DAVID (v. 6.7 Available from
http://david.abcc.ncifcrf.gov/) to compare gene ontologies for the differentially
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expressed genes against the entire QPX transcriptome. Gene ontologies (GO-Fat) for
biological processes that were enriched (p < 0.05) were visualized using Revigo ().
Results
Gene discovery section (ASHTON) (Tables and graphs)
Differential Expression
Summary
Several GO pathways in detail
Virulence factors or other factors? (Table?)
Discussion
Conclusions
Acknowledgements
The emerging infectious marine diseases consortium provided funding for the
graduate course ‘Ecology of marine infectious diseases’ where the majority of this
work took place. (OTHER FUNDING?)
References
Supek F, Bošnjak M, Škunca N, Šmuc T.
"REVIGO summarizes and visualizes long lists of Gene Ontology terms"
PLoS ONE 2011. doi:10.1371/journal.pone.0021800
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