Molecular Biology Core


DNA Microarray

The Shared Resource provides a wide-range of DNA microarray technologies and formats for Cancer Center investigators to perform high- and low-density gene expression profiling studies, alternative-splice analysis, genotyping, and measurement of copy number variation. Services include:

Array Production and Custom Printing. Human (18K) and mouse (22K) long-oligonucleotide (65-mers) libraries from Compugen Inc. (Rockville, MD) are used for the synthesis of high- (genome-wide expression profiling) and low- (customized) density arrays. These microarrays include a set of two 10K human oligionucleotide gene expression and discovery arrays, a 13K human oligonucleotide array of “known” genes, and a set of two 12K mouse oligonucleotide arrays, as well as investigator-initiated customized arrays. Sequence information for each oligonucleotide target in the libraries and/or investigator submitted sequences (i.e. alternative splicing surveys) provides for rapid synthesis and creation of custom printing plates and arrays by the Shared Resource. Each printed array is $40 to Cancer Center investigators.

Array Processing. Depending on the amount of investigator-isolated RNA and the selected DNA microarray format, the Shared Resource has established relevant protocols and performs the services of cDNA or amplified cRNA synthesis, fluorescent-labelling, hybridization, and processing of microarrays to Cancer Center investigators (typically $140-$170/array).

Array Analysis. The Shared Resource performs the services of initial data acquisition and first-tier analysis of hybridized arrays to Cancer Center investigators. This first-tier analysis involves scanning, digitizing, and segmenting images, determining expression and noise levels, scaling, and calculation of normalized expression ratios by microarray analysis specific software (typically $115-$135/array).

RNA Isolation, Purification, and Analysis ($125/sample).

Personnel Training. The Shared Resource provides training to investigators engaged, or interested, in DNA microarray-based research. This training includes assistance in designing and conducting array-based experiments, protocols for procurement of RNA samples from cells, tissues, and laser capture micro-dissected material, protocols for labeling targets and hybridizing arrays, and access to and training on core equipment and informatics software.