A common reference for cDNA microarray hybridizations.

Reliability of gene expression ratios for cDNA microarrays in multiconditional experiments with a reference design.

In a typical gene expression profiling experiment with multiple conditions, a common reference sample is used for co-hybridization with the samples to yield expression ratios. Differential expression for any other sample pair can then be calculated by assembling the ratios from their hybridizations with the reference. In this study we test the validity of this approach. Differential expression ...

Characterization of gene expression profiles of normal canine retina and brain using a retinal cDNA microarray.

PURPOSE Construction of a canine retinal custom cDNA microarray for comprehensive retinal gene expression profiling and application for the identification of genes that are preferentially expressed in the retina and brain lobes using a brain pool reference tissue. METHODS A cDNA microarray was constructed utilizing clones obtained from a normalized canine retinal expressed sequence tag librar...

Materials and Methods MICROARRAY CONSTRUCTION AND DATA ACQUISITION

MICROARRAY CONSTRUCTION AND DATA ACQUISITION cDNA microarrays were constructed with ~9,700 Drosophila cDNA elements representing 5,081 different genes. We sequenced the 5’ ends of 80% of the cDNAs to verify their identities. The results considered below are for the 4,028 sequence-verified, unique genes. Poor quality spots on the microarrays were filtered from the raw data before analysis. A spo...

cDNA Microarray Data Normalization

Dye bias correction in dual-labeled cDNA microarray gene expression measurements.

A significant limitation to the analytical accuracy and precision of dual-labeled spotted cDNA microarrays is the signal error due to dye bias. Transcript-dependent dye bias may be due to gene-specific differences of incorporation of two distinctly different chemical dyes and the resultant differential hybridization efficiencies of these two chemically different targets for the same probe. Seve...