1. Microarray:

• RNA integrity analysis

• RNA sample labeling

• Microarray hybridization

• Image scanning and feature extraction

• RT-PCR validation

EHS Center members have the option of using MBFC resources and personnel in a full-service manner, or they may choose to perform microarray experiments and analyses themselves using MBFC facilities. In the former case, investigators typically submit mRNA samples, and MBFC personnel perform the associated mRNA integrity analysis, labeling, hybridization, and imaging. Sample integrity analysis is accomplished using the Agilent Bioanalyzer. In most cases, the MBFC will complete full service microarray work and preliminary data analysis within seven days, starting from the scheduled experiment start date. MBFC personnel with technical expertise in microarray protocols are available to assist and train investigators who desire to perform their own experiments using MBFC resources. All reagents required to perform microarray experiments are available through the MBFC, some at discounted prices. The MBFC offers cDNA and oligo arrays for numerous organisms, as well as custom designed microarrays. In addition, microarray results can be validated using TaqMan RT-PCR technology available through the MBFC.

2. Bioinformatics:

• Microarray data storage and management

• Statistical analysis

• Data clustering

• Biological pathway analysis

• Categorization and annotation of microarray data

• Public database mining

The MBFC provides exceptional bioinformatics resources to facilitate the effective management and analysis of microarray data. Central to the MBFC data analysis pipeline is Rosetta Resolver®, a premier server-based microarray database and analysis package that has high-throughput capacity and advanced data analysis tools. Integral to Resolver is a high-capacity Oracle database for microarray data management. Using Resolver, investigators store their microarray images and data on the MBFC microarray server then conveniently access and analyze the data from their own labs via the internet. The Resolver system is seamlessly integrated with the Agilent microarray platform. EHS investigators have the benefit of a high-end microarray analysis system but are relieved of the hardware and software overhead required for effective data management, storage, backup, and analysis.

Link to Rosetta Resolver Web Site

3. Other Services Available Through the University Genomics Facility:

Affymetrix GeneChip Analysis: Microarray experiments can be performed using Affymetrix technology to quantify gene expression in user-supplied samples.

Fluorescent Chromosome Analysis: Simultaneous 24-color fluorescent in situ hybridization of metaphase spreads. Useful when trying to detect or follow multiple chromosome translocations and marker chromosomes in a sample.

High Throughput DNA Genotyping/Sequencing: Depending on project size, sequencing using ABI 377 instruments or the new ABI 3700 sequencer is available. The latter instrument will sequence/genotype 950 cDNAs per day from 96 titer well dishes using fiber optic capillaries.