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| Status |
Public on Jun 01, 2006 |
| Title |
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.
This SuperSeries is composed of the SubSeries listed below.
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| Overall design |
Refer to individual Series
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| Contributor(s) |
Kuo WP, Liu F, Cepko CL, Jensen T, Ohno-Machado L, Bumgarner R, Choi S, Church GM, Jensen R, Kim J, Perrin S, Ricciardi-Castagnoli P, Seed B, Hovig E, Punzo C, Lombardi M, Sarang J, Maysuria M, Serikawa K, Lee SY, McCrann D, Kang J, Shearstone J, Burke J, Park D, Wang X, Short G, Freeman M, Trimarchi J, Whipple ME, Rector T |
| Citation(s) |
16823376 |
| Submission date |
May 16, 2006 |
| Last update date |
Feb 18, 2018 |
| Contact name |
Winston Patrick Kuo |
| E-mail(s) |
wkuo@genetics.med.harvard.edu
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| Organization name |
Harvard Medical School
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| Department |
Genetics
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| Lab |
Cepko
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| Street address |
188 Longwood Avenue
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platforms (9)
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| GPL81 |
[MG_U74Av2] Affymetrix Murine Genome U74A Version 2 Array |
| GPL922 |
Agilent-011472 Mouse Development Oligo Microarray G4120A (Feature Number version) |
| GPL2995 |
ABI Mouse Genome Survey Microarray |
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| Samples (91)
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| This SuperSeries is composed of the following SubSeries:
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| GSE4829 |
ABI experiments for cross-platform study |
| GSE4830 |
Affymetrix experiments for cross-platform study including site 2 data |
| GSE4831 |
Agilent experiments for cross-platform study |
| GSE4832 |
cDNA (Cepko BMAP) experiments for cross-platform study |
| GSE4833 |
Massachusetts General Hospital (MGH) long oligo experiments for cross-platform study |
| GSE4834 |
MWG BioTech experiments for cross-platform study |
| GSE4835 |
GE Healthcare (Amersham) experiments for cross-platform study including site 2 data |
| GSE4836 |
Operon/Compugen experiments for cross-platform study |
| GSE4837 |
Mergen experiments for cross-platform study including site 2 data |
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| Relations |
| BioProject |
PRJNA95853 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE4854_RAW.tar |
500.9 Mb |
(http)(custom) |
TAR (of CEL, TIFF) |
| Raw data provided as supplementary file |
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