Plans for Class on February 7th

On Tuesday we’re going to talk about how you work with sequence data, we’re going to get a chance to work with an example dataset and we’re going to have a discussion, led by Kris Voss about how we analyze community datasets.  This is your chance to learn a whole lot of acroynyms: PLFA, T-RFLPS, DGGE, phylochip, NMS, CCA, PCA – woo hoo!

In preparation for class all of you should read 2 papers that you can download here

Everyone Reads: Cao et al. Community Analysis Based Methods.  Chapter 11 in C. Hagedorn et al. (eds.), Microbial Source Tracking: Methods, Applications, 251pp

Table 1:  (that’s Kris, Alyse, Charlotte, Maria & Gillian) should read the Fang et al. 2001 paper about soil microbial community analysis using FAME and BIOLOG

Table 2: (that’s Auriel, Matt, Michael, Harrison & Katy) should read Braker et al. 2001 about sediment community analysis along redox gradients using T-RFLP analysis of 16s rRNA and nirS genese.

Table 3: (that’s Scott, Jeremy, Ryan, Lisa, and Kylie) should read Gotelli et al. 2011 which examines soil rhizosphere communities using 454 sequencing of 16s rRNA region for bacteria and D1/D2 region for fungi

Our goal for Tuesday will be to understand the kinds of information that can be generated about microbial communities using these different approaches and the ways in which community data can be analyzed and presented.  Think hard about the pros and cons of the approaches you are reading about in your table specific paper.  Come to class prepared to present your paper to peers.

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