Oklahoma State University
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Facility Description of Equipment, Software, Training and Services:


Summary of Services [PDF]


The Microarray Core Facility has excellent instrumentation for creating microarrays, performing hybridizations, and analyzing the results of microarrays. A complete list of hardware can be found online (http://microarray.okstate.edu/equipment.shtml). Available instruments include a GeneMachines OmniGrid 1000 contact printer, Axon 4400A four-laser high-resolution laser confocal scanner, incubators, ovens, and hybridization hardware. A Nanodrop-II non-contact nanoliter dispensing instrument (Innovadyne Technologies, Inc.) has been purchased to provide advanced arraying capabilities including the production of protein arrays, arraying into individual wells of 96-well plates, patterned dispensing of morphogens onto growth matrices, protein microcrystallography, and bead-based arrays.  NanoDrop ND-1000 spectrophotometers are available which are capable of full spectrum absorbance measurements using as little as one microliter of sample. Additionally a NanoDrop ND-3300 fluorospectrophotometer, also designed to use 1.5 microliter volumes, can provide full-spectrum excitation and full-spectrum emission wavelength plots for fluorescent samples. Recent acquisition of a suite of cell & tissue disruption equipment are hoped to allow training and consistency in the preparation of high-quality RNA and proteins.


The OMCF also provides computer time to registered users for microarray and macroarray image analysis and data processing. They are loaded with software for first, second and third level microarray data analysis. Software packages installed on these computer include Axon's GenePix Pro, ScanArray, ImaGene and ScanAlyze for first level analysis and MEV4, GeneSpring, Acuity, QuantArrray, R-Package with BioConductor, GeneSight-Lite, Genesis, Cluster and TreeView for second and third level microarray data analysis. In addition, we have developed an online program called GenePix Auto-Processor or GPAP for robust pre-processing and statistical analysis of raw microarray data. GPAP also provides diagnostic plots to evaluate the data quality and monitor the effects of pre-processing and normalization methods.


Collectively the Facility has performed gene expression studies, hybridization experiments, image acquisition and/or associated analyses in multiple model systems including Aspergillus, Bermuda grass, Campylobacter, cotton, cows, humans, mice, pigs, dogs, rats, sorghum, Synechocystis, ticks, tomatoes, various bacteria, viruses and wheat. The Facility provides service and training for microarray fabrication and image acquisition. The Facility also provides training, technical support and recommendations for all aspects of microarray-base studies including labeling, hybridization and data analysis while providing consultation for experimental design, projects and proposal development. We appreciate your interest and look forward to assisting you in the near future.