Affymetrix User

1
Affymetrix Users 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

2

• 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

3

• 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 Post-mortem 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

4
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