Transcript Holly_060605 - Personal.psu.edu

Affymetrix User’s Group Meeting
Boston, MA
May 2005
Keynote Topics:
1. Human genome annotations: emergence of non-coding transcripts
-tiling arrays: study gene regulation (complement expression arrays),
explore genome functions including: DNA methylation, origins of replication,
mapping sites of TF binding
2. mRNA transcript variation across ‘druggable’ genome: novel targets
from exon array data
- exon arrays: study alternative splicing, explore transcript based pathways vs
gene based pathways
3. Enabling microarrays for routine clinical use
-personalized medicine
-example = SNP chips (mapping & linkage analysis)
-10K, 100K & 500K SNP chips
- Serono Identifies 80 genes involved in MS using 100K SNPs
Data Analysis Track:
1. Microarray Expts: Conceptual view & Practical Considerations
- Experiment design-begin w/end in mind, focus on questions seeking to be
addressed & have specific goals (i.e. transcriptional changes vs cluster analysis)
- Replicates: biological vs technical, no need for technical replicates if sample
preparation, etc is done consistently, # of biological replicates depends on focus
of experiment, pooling – suppresses changes
- data analysis: 1) look at the data statistically 2) look at the data biologically
2. Plier algorithm: higher differential sensitivity for low expressors
- signal detection algorithm
- normalization
- background correction (PM-MM)
3. Statistical tools & data visualization
- RMA = robust multi-chip average
- T-test (ANOVA) – compare signal across biological replicates
- software
Software
Affy Array Assist Lite (Stratagene)
– download for free off Affymetrix website (www.affymetrix.com)
Poster
Effects of RNA Degradation on Gene Expression Analysis of Human Postmortem Tissues
– Jerry Lee, Dept of Molecular Medicine, Neurocrine Biosciences, Inc.,
San Diego, CA
- Summary: RNA from Human Brain (and other tissues) & RNA from Rat
duodenum was used to address how RNA quality affects gene expression data
generated using Affy chips
– Conclusion: Degraded RNA gave comparable signal to “good quality” RNA
Effects of Exercise on Gene Expression in Bone & Brain Tissues
from different strains and sexes of mice
Updates:
1. Exercise Program (sufficient to produce significant changes in skeletal system)
-mice ~6 months old (growth should have stopped)
-mice randomly selected to exercise
-10 degree incline (treadmill design)
-exercise during dark cycle (when mice naturally more active)
-30 min/day, 5 days/wk, 6 wks total
2. Experimental Considerations
a. RNA quality
b. # of replicates/pooling
c. chip array type? ($175 price difference)
1. 430A 2.0 - $350/chip, 14,000 genes
2. 430 2.0 - $525/chip, 39,000 transcripts