E-TABM-16 - Platform comparison and transcription profiling of mixed tissue RNA samples formulated to contain different ratios of RNA for each of four rat tissues (brain, liver, kidney, and testes) on Affymetrix RAE230A, CodeLink UniSet Rat I, and Agilent G4130A rat oligonucleotide arrays

Status
Released on 30 March 2010, last updated on 12 October 2011
Organism
Rattus norvegicus
Samples (6)
Arrays (3)
Protocols (37)
Description
This experiment is a test of a reagent that can provide a basis for performance assessments on Affymetrix RAE230A, CodeLink UniSet Rat I, and Agilent G4130A rat oligonucleotide arrays. The reagent is a set of two mixed tissue RNA samples formulated to contain different ratios of RNA for each of four rat tissues (brain, liver, kidney, and testes). The analytes in this assay bind to a subset of gene probes that were matched across platforms to the same UniGene cluster or GenBank accession number, were determined to be tissue-selective on each of the 3 platforms using average baseline expression levels in single tissue samples from control animals, and have signal intensities that span the dynamic range of each platform. This reagent forms the basis of a ratiometric assay in a complex biological background that can be used to objectively assess the effect of different array processing methods and conditions on microarray data comparability within and across platforms, and could be a paradigm for similar performance standards for mouse and human arrays.
Experiment types
transcription profiling by array, quality control testing
Contact
Citation
Use of a mixed tissue RNA design for performance assessments on multiple microarray formats. Thompson, Karol L.; Rosenzweig, Barry A.; Pine, P. Scott; Retief, Jacques; Turpaz, Yaron; Afshari, Cynthia A.; Hamadeh, Hisham K.; Damore, Michael A.; Boedigheimer, Michael; Blomme, Eric; Ciurlionis, Rita; Waring, Jeffrey F.; Fuscoe, James C.; Paules, Richard; Tucker, Charles J.; Fare, Thomas; Coffey, Ernest M.; He, Yudong; Collins, Patrick J.; Jarnagin, Kurt; Fujimoto, Susan; Ganter, Brigitte; Kiser, Gretchen; Kaysser-Kranich, Tamma; Sina, Joseph; Sistare, Frank D.
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-TABM-16.idf.txt
Sample and data relationshipE-TABM-16.sdrf.txt
Raw data (1)E-TABM-16.raw.1.zip
Array designsA-AFFY-25.adf.txt, A-AGIL-6.adf.txt, A-MEXP-124.adf.txt
Links