OHSU

Equipment & Protocols

equipment

Affymetrix GeneChip® Instrument System

The Affymetrix GeneChip Instrument System is designed for use with Affymetrix GeneChip® expression probe arrays and Genotyping assays.  The system includes the two-color GeneChip Scanner 3000 with AutoLoader, three Fluidics Station 450s, Hybridization Oven 645, a powerful computer workstation with Affymetrix GeneChip Operating System (GCOS) and GeneChip Command Console Software (AGCC), and scanner workstation with a 2D handheld barcode reader. 

The Affymetrix Microarray Core maintains a full service agreement on the instrument system and adheres to a strict instrument maintenance and test performance regime including an ongoing, monthly assay stability study.

Agilent 2100 Bioanalyzer

Agilent's 2100 Bioanalyzer uses a lab-on-a-chip approach to perform fluorescence-based capillary electrophoresis to assess starting sample integrity.  A concentration measurement is also generated, which is compared against optical density (OD) measurements obtained from the NanoDrop-1000/8000 spectrophotometer.  The Bioanalyzer uses two chip types: the Nano LabChip (25 ng/μl - 500ng/μl input RNA) and the Pico LabChip (50pg/μl - 5000pg/μl input RNA). 

Molecular Devices SpectraMax M2 Plate Reader

SpectraMax M2 from Molecular Devices is a multi-detection microplate reader with dual-monochromators and dual-mode cuvette ports.  Detection modalities include absorbance (UV-Vis Abs) and fluorescence intensity (FI).  The system has optical performance comparable to a top-of-the-line dedicated spectrophotometer or spectrofluorometer and can read 6- to 384-well microplates.

NanoDrop 8000 Spectrophotometer

The NanoDrop 8000 spectrophotometer takes full-spectrum UV-Vis absorbance measurements of up to eight samples simultaneously, utilizing only 1μl of volume per sample read.  Using an eight channel pipette to dispense samples on a linear array of pedestals, 96 samples may be measured in less than six minutes. 

Thermocyclers

The core uses multiple MJ Research Peltier Thermal Cycler DNA Engine Tetrad (PTC-225) machines. 

Core Protocols

Affymetrix Microarray Core Hybridization Naming Schema
Need to decode an AMC ID?  This links to information about how the AMC names hybridizations and why the schema is used.

Affymetrix Microarray Core 3'IVT Expression Assay Methods v2.0_Affymetrix Kit Labeling Assay
This document provides a brief description of methods used in the AMC laboratory for sample labeling and array hybridization and processing during the period of June 2004 through September 2007 for GeneChip arrays with feature sizes greater than or equal to 11-micron (e.g, HG-U133 Plus 2.0,MOE 430 2.0). 

Affymetrix Microarray Core Labeling Methods v1.0_Standard Labeling Assay
This document provides a brief description of methods used in the AMC laboratory for sample labeling and array hybridization and processing during the period of Jan 2002 through June 2004 for GeneChip arrays with feature sizes greater than or equal to 18 micron (e.g, HG-U133A, MOE430A, MG-U74A).  Note: for sample inputs of less than 4?g or assays with GeneChip 2.0 all-on-one arrays, the protocols described in this document are not accurate.  

If you have questions about methods or require additional information, please contact the Core Director.  For manuscript preparation, we recommend confirming final methods text with a member of the Affymetrix Microarray Core.  Contact us.