The Affymetrix GeneChip® Analysis System uses application-specific high-density GeneChip® oligonucleotide probe arrays to efficiently acquire and analyze genetic information for gene expression, genotyping and nucleotide variant detection. This multi-component system includes two GC450 Fluidics Stations, a Hybridization Oven 640, a GC3000 7G scanner, computer workstation, and GeneChip® Operating Software v1.4 (GCOS). The GCOS software automates control of the GC450 Fluidics Stations and the GC3000 7G scanner, captures GeneChip probe data and uses algorithms to analyze the hybridization intensity data. GCOS uses algorithms to determine absolute or comparison gene expression results, perform nucleotide variant detection, or identify genotype, depending on the type of probe array assay. Software for data analysis can be accessed in the Gene Expression Center.

The University of Wisconsin-Madison receives an Academic Access discount (Tier III) on all Affymetrix GeneChips®. When ordering from Affymetrix, please refer to UW Contract #27465 to ensure this pricing. Please refer to the current UW-Madison Affymetrix Price Sheet for all GeneChip® prices.   

                                                     Images courtesy of NimbleGen

           NimbleGen 12 Bay Hybridization System

The system  insures reproducible NimbleGen array results by maintaining a constant temperature, and providing active mixing of the hybridization cocktail. This mixing is tied to the use of NimbleChip Mixers. These Mixers adhere directly to your array, before sample loading and hybridization.

The Bioanalyzer utilizes 'Lab-on-a-Chip' technology to integrate sample preparation, fluid handling, separation, detection, and data analysis. Providing researchers with standardized methods and enhanced reproducibility. Each chip contains an interconnected set of gel-filled channels that allow for molecular sieving of nucleic acid and protein samples.

Quick and Easy Operation

* Simple chip preparation requires less than 5 minutes set-up time.
*Ready to use reagent kits.
*Only 1ul of sample required (25-500ng/ul RNA, 0.5-50ng/ul DNA)
*Only 30 minutes to run and analyze 12 samples.
*Data is displayed as a gel-image or electropherogram
*Automatically calculates fragment size, concentration, ribosomal RNA ratios,
*High detection sensitivity. More sensitive than a polyacrylamide gel stained with EtBr or SYBR

  Gold.
*Built in quality control with custom array ladders.

Currently, Agilent has LabChip kits that can analyze RNA, DNA, and Proteins. Some examples of analysis that can be done are: quantitative analysis of PCR fragments, restriction fragment sizing, Cy5 labeled cRNA and cDNA. RNA analysis up to 6,000 bases. DNA analysis from 25-12,000bp. Analyze protein samples ranging in size from 14 to 200 kDa including cell lysates, column fractions, and purified proteins.

THIS INSTRUMENT IS AVAILABLE TO ALL UW-MADISON RESEARCHERS

There is a one time training fee of $90.00.

Interested users may purchase their own kits or purchase single chips from the Center.

For more information visit the Agilent web site: http://www.agilent.com/chem/labonachip

Or contact: gecinfo@biotech.wisc.edu

• Nucleic acid concentration and quality of nucleic acid samples up to 3700 ng/ul (dsDNA) without dilution
• Fluorescent dye labeling density of nucleic acid microarray samples
• Protein analysis (A280) up to 100 mg/ml (BSA)
• Bradford Assay analysis of protein
• Cell density measurements
• General UV-Vis spectrophotometry

Access to the NanoDrop® is free of charge to GEC facility users. 

Molecular Devices Axon4000B Scanner

The Molecular Devices Axon4000B scanner features high speed simultaneous dual-channel scanning that elimates the post-capture image registration, avoids pixel shifting and increases acquistition speed (~5 minute scan for two wavelengths at 10um resolution).  The Axon4000B is used in conjuction with GenePix® Pro 6.0 software for the analysis and visualization of each scanned microarray.  The Axon4000B is available for analysis of custom designed and commercially available high-density microarrays.

The PerkinElmer ScanArray Express, formerly GSI, is a scanning laser confocal fluorescence microscope that is able to determine the fluorescence intensity of a two dimensional array of spots on a microarray. The ScanArray® Express is configured with four lasers, three internal and one external, along with various excitation and emission filters to allow the user to utilize a broad range of fluorophores. The ScanArray Express® is used in conjunction with QuantArray for quantitation, processing, reporting and storage of data. The PerkinElmer ScanArray® Express is available for analysis of custom designed and commercially available high-density microarrays.

The Gene Machines OmniGrid Arrayer, from Genomic Solutions, is a high performance, multi-axis robot that is capable of arraying biological samples from standard 96 and 384-well sample plates onto up to 100 glass microscope slides. The standard spot size per sample is ~100 microns. Spot densities of >5,000 spots / 2cm squared are currently achievable. Spotting relies on TeleChem SMP3 quill-like pins, which load 0.2 - 0.5 ul from each source well and deposits approximately a nanoliter spot on each slide. The software provided with the Omni Grid is user-friendly and allows for a large amount of flexibility in printing.