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Series GSE4829 Query DataSets for GSE4829
Status Public on Jun 01, 2006
Title ABI experiments for cross-platform study
Organism Mus musculus
Experiment type Expression profiling by array
Summary Gene expression microarrays have made a profound impact in biomedical research. The diversity of platforms and analytical methods has made comparison of data from multiple platforms very challenging. In this study, we describe a framework for comparisons across platforms and laboratories. We have attempted to include nearly all the available commercial and “in-house” platforms. Using probe sequences matched at the exon level improved consistency of measurements across the different microarray platforms compared to annotation-based matches. Generally, consistency was good for highly expressed genes, and variable for genes with lower expression values as confirmed by QRT-PCR. Concordance of measurements was higher between laboratories on the same platform than across platforms. We demonstrate that, after stringent pre-processing, commercial arrays were more consistent than “in-house” arrays, and by most measures, one-dye platforms were more consistent than two-dye platforms.
Keywords: cross platform microarrays
 
Overall design RNA samples used were aliquoted from two pools of samples: C57/B6 adult mouse retina (MR) and Swiss-Webster postnatal day one (P1) mouse cortex (MC). The mouse cortex was used as a reference sample for the dual-dye platforms.Five replicates of each sample were used to assess the degree of variation in the expression data within each platform.
 
Contributor(s) Kuo WP
Citation(s) 16823376
Submission date May 14, 2006
Last update date Mar 17, 2012
Contact name Winston Patrick Kuo
E-mail(s) wkuo@genetics.med.harvard.edu
Organization name Harvard Medical School
Department Genetics
Lab Cepko
Street address 188 Longwood Avenue
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platforms (1)
GPL2995 ABI Mouse Genome Survey Microarray
Samples (10)
GSM108110 ABI-MC-1
GSM108116 ABI-MC-2
GSM108118 ABI-MC-3
This SubSeries is part of SuperSeries:
GSE4854 Cross-platform study
Relations
BioProject PRJNA104555

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