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| Status |
Public on Jun 01, 2006 |
| Title |
ABI experiments for cross-platform study |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
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| 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
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| 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.
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| 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
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| 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 |
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| Platforms (1) |
| GPL2995 |
ABI Mouse Genome Survey Microarray |
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| Samples (10)
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| This SubSeries is part of SuperSeries: |
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| Relations |
| BioProject |
PRJNA104555 |
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