Methods - Affymetrix analysis
Target Preparation and Hybridization
All protocols were conducted as described in the Affymetrix GeneChip Expression Analysis Technical Manual. Briefly, XXug of total RNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP. The cRNA products were fragmented to 200 nucleotides or less, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to XXXX microarrays. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. A confocal scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.
Initial Data Analysis
Affymetrix Microarray Suite 5.0 was used to quantitate expression levels
for targeted genes; default values provided by Affymetrix were applied
to all analysis parameters. Border pixels were removed, and the average
intensity of pixels within the 75th percentile was computed for each probe.
The average of the lowest 2% of probe intensities occurring in each of
16 microarray sectors was set as background and subtracted from all features
in that sector. Probe pairs were scored positive or negative for detection
of the targeted sequence by comparing signals from the perfect match and
mismatch probe features. The number of probe pairs meeting the default
discrimination threshold (tau = 0.015) was used to assign a call of absent,
present or marginal for each assayed gene, and a p-value was calculated
to reflect confidence in the detection call. A weighted mean of probe
fluorescence (corrected for nonspecific signal by subtracting the mismatch
probe value) was calculated using the One-step Tukey's Biweight Estimate.
This Signal value, a relative measure of the expression level, was computed
for each assayed gene. Global scaling was applied to allow comparison
of gene Signals across multiple microarrays: after exclusion of the highest
and lowest 2%, the average total chip Signal was calculated and used to
determine what scaling factor was required to adjust the chip average
to an arbitrary target of 150. All Signal values from one microarray were
then multiplied by the appropriate scaling factor.
Last Updated on 9/3/03
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