BME/BIOL 210: Experimental Systems Biology
Fall Quarter, 2008
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
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 &
(2) technology to be used (why is this an effective
use of this technology? why is it better than a traditional molecular
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
(1) Array platform, type of probes, approximate cost
(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
D. Analysis Plan
(1) What tools/program will you use to analyze your
(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).