Equipment and Database Tools
Flexys Microgridding Robot
The Microarray Core Facility uses the Flexys microgridding robot (Genomic Solutions, Inc.) for printing cDNA clones. The notable features of this robot include a 48-pin printing head with solid pins, eight 384-well plate input capacity and a 24-slide printing capacity at any given time. The solid pins eliminate sample carry-over between clones and facilitates reproducible deposition of samples between slides. The robot is equipped with a sonicated bath and heated drying set-up to facilitate effective washing of pins between samples. The 48-pin print head makes this robot suitable for high-density arraying of cDNA clones. The software enables choice of varying distance between spots, different printing patterns and multiple transfers to individual spots.
Flexys Microgridding Robot (ppt)
GenePix 4000
The Microarray Core Facility uses a dual-laser scanner, GenePix 4000 (Axon, Inc.) for quantitation and analysis of results. The slides are scanned for the Cyanin-3 and Cyanin-5 signals and a composite image is produced. The different spots appear in different shades varying from green (for a gene that is under-expressed in the treated sample) to red (for a gene that is over-expressed in the treated sample). A yellow signal indicates unchanged expression for a gene. The data are represented as a ratio of the two signals Cyanin-5 (emmision 635 nm; red fluorescence) to Cyanin-3 (emmision 532 nm; green fluorescence).
GenePix 4000 (ppt)
Affymetrix GeneChip® System
The Affymetrix GeneChip® System consists of a hybridization oven, the GeneChip® Fluidics Station, GeneArray™ Scanner and a computer hosting the Microarray Suite software.
The Hybridization Oven 640 automates the hybridization process for GeneChip® probe arrays. The oven provides precise temperature control to ensure successful hybridization and cartridge rotation to provide continuous mixing. Up to 64 arrays can be processed at one time. The digital speed control display enables the selection of specific rotation speeds.
The GeneChip® Fluidics Station automates the delivery, timing and temperature control of reagents for staining and washing of the probe arrays. Each fluidics station can independently process four arrays at one time.
Once the end user provides the information about the type of array, the software automatically selects the appropriate protocol. Once processing is complete, messages are displayed on the PC and the fluidics station that the probe array is ready for scanning.
The GeneArray™ Scanner uses an argon-ion laser to excite fluorescent molecules incorporated into the nucleic acid target to generate a quantitative hybridization signal. With precise optics, the GeneArray™ scanner focuses the laser on 3-micron spots within each of the thousands of probe features contained on the GeneChip® probe array. A high-resolution image of the probe array is displayed in real time during scanning, and fluorescence intensity data is automatically stored in a raw file.
The Microarray Suite software provides centralized instrument control for both the fluidics station and the GeneArray™ Scanner. The Microarray Suite software interface supports instrument control, array image acquisition, and communication with the Affymetrix LIMS software for data storage. All functions are displayed in the user interface using multiple toolbar displays, allowing one to locate and analyze data. Images of scanned arrays can be viewed in a multitude of ways including several images at a time. While viewing the array image, interactive pop-up windows provide access to information such as probe hybridization intensity and probe cell information.
The Microarray Suite software also supports viewing of distributed probe set arrays, where all probes in a set are placed in different areas of the array. When running in LIMS Mode and communicating with a LIMS server, the Microarray Suite software allows one to publish data, set up experiments, define sample attributes, monitor the experiment workflow queue, and access sample history information.
Affymetrix GeneChip System (ppt)
Piezorray (PerkinElmer)
The Piezzorray is a non-contact microdispensing system designed specifically for pipetting sub-nanoliter volumes to dense arrays. Liquid volumes are controlled by a piezoelectric tip technology that dispenses 333 picoliter volume droplets. The instrument is versatile, being able to pipette into and aspirate out of a number of standard plate formats, and dispense to a variety of porous and non-porous substrates for creating arrays. The Piezorray is controlled by an external computer. The base unit contains one source plate holder, an ultrasonic washbowl, a computer and a monitor, and a bottle for system liquid.
Agilent 2100 Bioanalyzer (AgilentTechnologies)
The Agilent 2100 Bioanalyzer is a microfluidics-based platform for the analysis of DNA, RNA, proteins and cells. This instrument is used for checking the integrity of the samples. Microfluidics cartridges are used to analyze 10-12 samples simultaneously. This instrument replaces the use of gel electrophoresis for checking samples integrity for nucleic acids and proteins.
Maui Hybridization System
The Maui 4-Bay Hybridization System (BioMicro Systems) is a hybridization station that allows simultaneous hybridization onto four standard glass slides. The Microarray Core Facility uses the hybridization system for both NimbleGen and Exiqon microarray. Samples are hybridized onto microarrays using NimbleChip Mixers, a line of adhesive sample enclosures that provide containment and active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal. The mixers allow for a reduction of hybridization volume (down to 38 ml), leading to greater sensitivity and reliable results while economizing on sample requirements.
Biomek FXP Laboratory Automation Station (Array Plex-SA)
The Biomek FXP Laboratory Automation Station (Array Plex-SA) automates target preparation steps for Affymetrix microarrays in a standard 96-well format. Starting with total RNA, it can process eight to 96 samples for target preparation in less than 48 hours. It requires 1-5 µg of total RNA for target preparation and yields 30-80 mg of biotinylated cRNA for hybridization to microarrays. All the reagents are supplied to the robot as master mixes at the beginning of a run. The entire process is performed with very minimal user intervention. This automated system will enable the core to expedite samples handling for the users and will potentially decrease variability between samples due to minimal manual steps involved. The only method currently automated on the robot is the IVT process (one-cycle procedure). The protocols for SNP genotyping will be automated in the near future.
Database Tools
Laboratory Information Management System (LIMS)
Services from the MCF should be requested through the LIMS (only for M. D. Anderson employees). The LIMS offers the users an easy way to track the status of their projects and services requested from the Microarray Core Facility. Every user is first required to submit a project for which services will be requested. All submitted projects are reviewed at three levels – science, technology and statistics. Services can be requested only for projects approved at all the three levels. Please read the LIMS user manual (doc) [link file] for details.
Contact Information
Mini Kapoor, Ph.D.
Assistant Professor
Department of Molecular Genetics
Phone: (713) 834-6382
Project Tracker
This is a tool constructed by the Department of Biostatistics at The University of Texas M. D. Anderson Cancer Center. Project Tracker (only for M. D. Anderson employees) tracks the status of all genomics and proteomics projects handled by the core facilities at M. D. Anderson Cancer Center. Automated e-mails are sent to the principal investigator and all relevant personnel involved in a project in the event of a status change of the project.
Contact Information
Kevin Coombes, Ph.D.
Associate Professor
Department of Biostatistics
(713) 794-4154
GeneDirector
The microarray data is hosted in the database system, GeneDirector, from Biodiscovery, Inc.
GeneDirector is a suite of applications with the following components:
- GeneDirector data management - stores images and quantifications, allows data to be organized into experiments and projects and allows data to be shared to other users
- GeneSight - analysis program
- ImaGene - image quantification program (GeneDirector accepts quantifications from other programs as well, e.g., ArrayVision)
- CloneTracker - clone library/custom array management/tracking/design tool
All data is stored on an Oracle database back-end. More information on these products are available from BioDiscovery, Inc.
Contact Information
Sylvain Laroche
Systems Analyst
Department of Biostatistics