BME/BIOL 210: Experimental Systems Biology

Fall Quarter, 2008

          Pseudo grant

Topic & specific aims due for approval November 4th.
Due tuesday before thanksgiving break (November 25th).

Write up a 5-8 page pseudo-grant in which you describe a pilot study to be funded using high-throughput sequencing, microarray, or other functional genomics technology discussed in class or approved by me.  The study should be able to
be completed within 3-9 months, for a total budget of $35,000 or less.  Your goal is collect enough preliminary data to later be able to write a full-fledged grant for NIH or NSF funding for 3-5 years (not part of this assignment).

This pilot grant proposal will include:

A. Brief introduction
    (1) biological problem to be studied & importance/significance
    (2) technology to be used (why is this an effective use of this technology? why is it better than a traditional molecular biology technique?)
B. Specific Aim(s) - specifically state what you are trying to do.
       For example:  To measure stage-specific changes in host cell/tissue gene expression upon infection with Salmonella in order to identify
            genes involved in host immunological response.
C. Experimental Plan - Describe how you plan to carry out your array experiment, includeing
    (1) Array platform, type of probes, approximate cost per array
    (2) Experimental design: how many biological replicates or time-course samples taken & when, how many technical replicates, use of dye swaps
    (3) Types of postive or negative controls you plan to use
D. Analysis Plan
    (1) What tools/program will you use to analyze your data?
    (2) How will you assess the significance of your new gene list of interest?
E. Supporting, Follow-up, & Future experiments --
    (1) In the best array papers we've read in class, all have follow-up experiments to support major findings.  Propose at least two types of supporting non-array based experiments that could be done to increase the confidence in the array findings
    (2) If you can think of any computational / genomic / proteomic follow-up future studies that could leverage your new findings, describe them briefly (i.e., identifying new transcription factor binding sites, pathogenicty islands of genes that could be targetted for drug development, working out full pathways
using genetic screens, etc).