[Coral-List] gene expression analysis for marine biologists

[Mikhail Matz]

Dear colleagues,

Me and my PhD student Carly Kenkel are considering offering a "Gene expression analysis for marine biologists" workshop next summer, and I would greatly appreciate your opinion on what should we focus on: RNA-seq, qPCR, or perhaps both? 

RNAseq is a new global gene expression profiling method based on next-generation sequencing, it is basically the modern analog of microarrays. We have recently developed a modification of this procedure [1] that is simpler and much less costly than the original method, and it works very well in our hands and in several collaborating labs. Teaching RNAseq will involve substantial amount of bioinformatics, such as introduction to Unix, basic script writing, etc., in addition to wet lab procedures. 

While RNAseq is a great way to generate hypotheses, quantitative PCR (qPCR) is the way to test them. We have run qPCR workshops three times previously, and even published some of the results together with our students [2] (one more paper is in preparation). Please see http://www.bio.utexas.edu/research/matz_lab/matzlab/QPCR.html for the last year's course announcement and syllabus.

At the moment, I would greatly appreciate if you could write me back to indicate whether such a workshop sounds like a good idea in general, and if yes, what would be most useful subject, RNAseq, qPCR, or maybe both back to back, so the students could take one or the other or both.   

Please include "gene expression analysis for marine biologists" into the subject when replying.

Many thanks in advance,

Misha

References:
1. Meyer, E., Aglyamova, G. A., and Matz, M. V. Profiling gene expression responses of coral larvae (Acropora millepora) to elevated temperature and settlement inducers using a novel RNA-Seq procedure. Mol. Ecol. 2011, 17: 3599-3616.
2. Kenkel CD, Aglyamova G, Alamaru A, Bhagooli R, Capper R, Cunning JR, deVillers A, Haslun JA, Hédouin L, Keshavmurthy S, Kuehl KA, Mahmoud H, McGinty ES, Montoya-Maya PH, Palmer CV, Pantile R, Sánchez JA, Schils T, Silverstein RN, Squiers LB, Tang PC, Goulet TL and Matz MV. Development of gene expression markers of acute heat-light stress in reef-building corals of the genus Porites. PLoS ONE 2011, 6(10):e26914.

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Mikhail V. Matz
Associate Professor
University of Texas at Austin
Integrative Biology Section
1 University station C0930
Austin, TX 78712
phone 512-992-8086 cell, 512-475-6424 lab
fax 512-471-3878
web http://www.bio.utexas.edu/research/matz_lab