Microarray Core

Microarray

Services

GEP

Sample Drop-off

The Sample Drop-off room for the Microarray Core is located in Smith, room 1129. Please continue to send a completed application form to Core Director, Edward Fox.

More Info

To Use the Core

For instructions about how to use the Core, click here.

Gene Expression Profiling

A number of methods have been used to compare the absolute or relative expression of genes in two or more specimens. These include S.A.G.E. (Serial Analysis of Gene Expression), differential display, cDNA and oligonucleotide microarrays, and other methods. The Microarray Core offers a gene expression profiling service that uses oligonucleotide microarrays. Using this method, the RNA of interest is converted into cDNA, then amplified and labeled with biotinylated nucleotides by in vitro transcription to produce biotinylated cRNA. The cRNA is hybridized to a microarray chip. The bound cRNA is stained with fluorescent streptavidin. The microarray chip is then scanned using a laser, and the positions and intensities of the fluorescent emissions are captured. These measurements provide the basis of subsequent biostatistical analysis.

3' Arrays

The DFCI Microarray Core offers two different processing methods, referred to as Affymetrix process or NuGEN process, to covert RNA into biotinylated cRNA or cDNA, respectively, either of which is suitable for hybridization to the 3’ arrays.

Exon Arrays

All known and predicted exons are represented by four (>90% of exons) or less probes. The data from the arrays can either be used for generate whole transcript level or exon level expression values. The latter may permit identification of alternatively spliced transcripts. Mismatch (MM) probes are not present on the array. A “whole transcript (WT)” protocol (described below) is used to process submitted RNA. Exon arrays are available for human, mouse and rat profiling. Please see the Pricing page of this site for kind of chips that are available and for their prices.

Gene 1.0 ST Arrays

Each array of this type uses a subset of the probes from a corresponding Exon array to interrogate transcripts from approximately 28,000 well-annotated genes. Each transcript is probed by approximately 25 probes from exons distributed across the gene. Transcript level, but not exon level, expression values can be generated from the data. Mismatch (MM) probes are not present on the array. A “whole transcript (WT)” protocol (described below) is used to process submitted RNA. Exon arrays are available for human, mouse and rat profiling. Please see the Pricing page of this site for kind of chips that are available and for their prices.