1.  Genomic sequence of model eukaryote Saccharomyces cerevisiae completed in 1996. (12.1 Mb)  Despite 16 years of intense research, function of nearly 30% of putative open reading frames (ORFs) remain unknown.  In genomics, termed “ORFans”  Likely have function specific to fungi. Potentially important to food and drug industry.

2.  To determine the cellular function of a yeast ORFan gene by:  Reviewing basic gene information at yeastgenome.org  Analyzing data from a comparative RNAseq analysis of the deletion strain and the isogenic wild type strain to look for global changes in mRNA profiles  Grouping genes of similar expression profiles  Using pathway analysis to putatively link the ORFan to a Gene Ontology (GO) function. https://encrypted-tbn2.gstatic.com/images?q=tbn:ANd9GcQpx- HhripNInzlpjfIepFTmma0q8k-okvJq9_9Uml0SjsssDgPag

3.  Be able to access and use the basic search tools at yeastgenome.org  Understand the process of RNAseq analysis from RNA isolation through cDNA construction and sequencing.  Be able to load RNAseq data into the Galaxy platform for quality assessment, transcriptome alignment and differential expression analysis.  Be able to analyze differentially expressed genes for putative pathway placement.  http://craftbeeracademy.com/wp-content/uploads/2012/09/yeast_large_winter.gif

4. 1. ABILITY TO APPLY THE PROCESS OF SCIENCE: 2. ABILITY TO USE QUANTITATIVE REASONING : 3. ABILITY TO USE MODELING AND SIMULATION: 4. ABILITY TO TAP IN TO THE INTERDISCIPLINA RY NATURE OF SCIENCE: www.exploreyeast.com

5.  1. Ability to apply the process of science  Specifically, the ability to interpret and analyze data  2. Ability to use quantitative reasoning  Specifically, the understanding and using statistics to analyze data  3. Ability to use modeling and simulation  Specifically, the use of pathway analysis to assign gene function  4. Ability to tap into the interdisciplinary nature of science  Specifically, learning and using computational tools.  www.exploreyeast.com www.exploreyeast.com

6.  GCAT-SEEK sequencing requirements  Use of Illumina HiSeq  10-100 x 10 6 reads per sample, 50 – 150 nt  Do not need long sequencing runs for RNAseq  Program requirements for data analysis  Standard Mac or PC with internet access  Galaxy account (is this enough computing power for a yeast reference genome?)  Do not need to assemble because Saccharomyces reference genome is available www.mayo.edu

7.  Goals of yeast ORFan project:  organize a consortium of undergraduate researchers and PIs to assign functions to S. cerevisiae ORFans.  pilot project for summer of 2013  generate updated yeast ORFan list; draft a flow chart outlining process for determining the function of yeast ORFans  begin to work through the drafted process with three selected ORFans  design and begin RNAseq analysis of expression profiles in two ORFan deletion strains.  Full project: Students between consortium schools collaborate as teams to assign a gene ontology (GO) term to a given ORFan.  Ultimately, the yeast orphan gene project aims to use the process of determining ORFan gene function as a tool to gain experience in scientific research,  collaboration and leadership. www.bsse.ethz.ch