Friday Aug 17
Preparation and Discussion Time: Metagenomics (9:00-10:00)
Group Photograph (10:00-10:30)
Say "Bacterially-transformed milk product"
Student group presentations (10:30-11:30)
Send your presentation or link to google doc to Dana here: dana.s.brunson@gmail.com
6 min/group (~3 slides)
15 min at end for group discussion
Join.Me Session https://join.me/403-464-183
iPlant Atmosphere Wrap-up (11:30-12:00)
Closing down your Atmosphere VM
How to create and save a custom VM
Sharing a desktop environment with Atmosphere
Links
Lunch (12:00-12:45)
Introduction: Differential expression analysis (12:45-1:15)
Background: Comparative analysis of wild-type and hy5 mutant Arabidpsis.
HY5: Basic leucine zipper (bZIP) transcription factor. Nuclear localization. Involved in light-regulated transcriptional activation of G-box-containing promoters. Negatively regulated by Cop1. Although cytokinins do not appear to affect the gene's promoter activity, they appear to stabilize the protein. HY5 plays a role in anthocyanin accumulation in far-red light and blue light, but not in red light or in the dark. Mutant studies showed that the gene product is involved in the positive regulation of the PHYA-mediated inhibition of hypocotyl elongation. Binds to G- and Z-boxes, and other ACEs, but not to E-box. Loss of function mutation shows ABA resistant seedling phenotypes suggesting involvement for HY5 in mediating ABA responses. Binds to the promoter of ABI5 and regulates its expression.
(PDF 3.66 MB)
Reading Room
Good summary paper: http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html
Splicing-aware alignment to reference genomes: http://tophat.cbcb.umd.edu/
Assemble transcripts, estimate abundance, test diff. expression: http://cufflinks.cbcb.umd.edu/
Visualization of Tuxedo package results: http://compbio.mit.edu/cummeRbund/
BWA aligner http://bio-bwa.sourceforge.net/
De novo assembly with Trans-ABySS http://www.nature.com/nmeth/journal/v7/n11/full/nmeth.1517.html
De novo assembly with Trinity http://www.nature.com/nbt/journal/v29/n7/abs/nbt.1883.html
Differential expression analysis with iPlant (1:15-3:00)
Testing Opportunity iPlant is testing its new Discovery Environment 1.4 "Jacinthe" starting today. If you are comfortable with a slightly different interface, and are willing to put up with potential flakiness, I'm looking for ~10 volunteers to use the testing version of the DE for today's session.
Production Discovery Environment (1.21) http://de.iplantcollaborative.org/de/
Testing Discovery Environment (1.4a) http://dapple.iplantcollaborative.org/de/
Differential Expression Analysis Tutorial (Wiki. Semi-guided)
Feel free to stop when you get to the section RNA-Seq in Atmosphere.
Study Questions
Download your list of differentially expressed genes
Import it into a spreadsheet program (Google Docs, for instance).
Cut out the list of gene IDs. Submit it to the following web service
http://arabidopsis.org/tools/bulk/genes/index.jsp
Identify a couple of candidate genes that might lead to the hy5-215 phenotype pictured here
Workshop Wrap-up (3:00- )
Evaluation and feedback
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