IRP Microarray Core Facility - Services Provided

Labeling and Hybridization

The slides provided will be fully processed prints, ready for hybridization by the user. Current protocols describing methods for RNA isolation, production of labeled cDNA representations of the RNA, and hybridization will be available as text and in downloadable form the core web site. The core will provide hands-on training for first users. The user will be expected to provide all of the reagents called for in the protocol, for an experiment to be carried out at the core laboratory. However, it may be more practical for the first time user to consult with an Investigator whose laboratory is already undertaking microarray studies, and obtain more in-depth oversight of the experiments.

Laser Scanning

Two laser scanners are available at the core. However, because of the speed of the scanning (50 minutes each slide) the users will be required to reserve scanning time on the sign-up sheets for the scanners. The core will also provide technical advice on how to use the scanners. Once again, based upon the time demands on the core facility scanners, it may be more practical for investigators to arrange to use a scanner being used in individual laboratories already undertaking microarray studies, and obtain more in-depth oversight of the scanning and acquisition of data.

Data Analysis

The Bioinformatics Core will provide service and training for the primary data extraction and analysis of the microarray data as well as for the downstream analysis of interesting genes. The primary tool used for this process, and the only image software supported by the microarray core, is a suite of image analysis utilities called DeArray. Training in the use of more sophisticated analytical tools will not be provided, however, access to a variety of tools for gene and sample class discovery, and tools for examining the differential behavior of genes across samples is available via the internet.

Thus, in summary, the microarray core will provide arrays and advice/information about the use of microarrays. The preparation of samples, hybridization, data acquisition and analysis will be the responsibility of the Investigator.

Obtaining Arrays from the Core

NIMH investigators may contact Dr. Elkahloun directly to initiate microarray studies, but are encouraged to contact Dr. Samal in the NIMH Bioinformatics Core if they wish to discuss microarray platform options, experimental design, and post-array statistical and bioinformatics analyses

Lee E. Eiden, Ph.D. serves as the Chair of NIMH Microarray Users Committee. The information contained here has been largely derived from the NHGRI array core facility, and the assistance of Abdel. G. Elkahloun, Ph.D. , Microarray unit director, CGB-NHGRI-NIH is gratefully acknowledged.