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Use of a mixed tissue RNA design for performance assessments on multiple microarray formats.
- Source :
-
Nucleic acids research [Nucleic Acids Res] 2005 Dec 23; Vol. 33 (22), pp. e187. Date of Electronic Publication: 2005 Dec 23. - Publication Year :
- 2005
-
Abstract
- The comparability and reliability of data generated using microarray technology would be enhanced by use of a common set of standards that allow accuracy, reproducibility and dynamic range assessments on multiple formats. We designed and tested a complex biological reagent for performance measurements on three commercial oligonucleotide array formats that differ in probe design and signal measurement methodology. The reagent is a set of two mixtures with different proportions of RNA for each of four rat tissues (brain, liver, kidney and testes). The design provides four known ratio measurements of >200 reference probes, which were chosen for their tissue-selectivity, dynamic range coverage and alignment to the same exemplar transcript sequence across all three platforms. The data generated from testing three biological replicates of the reagent at eight laboratories on three array formats provides a benchmark set for both laboratory and data processing performance assessments. Close agreement with target ratios adjusted for sample complexity was achieved on all platforms and low variance was observed among platforms, replicates and sites. The mixed tissue design produces a reagent with known gene expression changes within a complex sample and can serve as a paradigm for performance standards for microarrays that target other species.
- Subjects :
- Animals
Gene Expression Profiling methods
Male
Oligonucleotide Array Sequence Analysis methods
Oligonucleotide Probes
RNA, Messenger metabolism
Rats
Rats, Sprague-Dawley
Reference Standards
Reproducibility of Results
Tissue Distribution
Gene Expression Profiling standards
Oligonucleotide Array Sequence Analysis standards
RNA, Messenger standards
Subjects
Details
- Language :
- English
- ISSN :
- 1362-4962
- Volume :
- 33
- Issue :
- 22
- Database :
- MEDLINE
- Journal :
- Nucleic acids research
- Publication Type :
- Academic Journal
- Accession number :
- 16377776
- Full Text :
- https://doi.org/10.1093/nar/gni186