Abstract: Comparative genomic hybridization is a tool that compares DNA samples from suspect cells of an organism with DNA samples from normal cells. Cross-species comparative genomic hybridization visualization allows genomic data from model organisms to be mapped and presented in accordance with the (for example) human genome to suggest possible common biological effects between two or more species.

Abstract: A method for determining chromatin accessibility of nucleic acids in a cell by expressing an effective amount of a nuclease in a cell to digest chromatin at chromatin accessible sites to form chromatin fragments; isolating chromatin fragments from the cell; and hybridizing the chromatin fragments on a microarray to determine the location and/or sequence of the chromatin fragments.

Abstract: Methods, compositions, and kits for performing a one-color analysis of microarray data are provided. Also disclosed are compositions including control nucleic acid sequences, and methods for measuring the dynamic range of a microarray analysis.

Abstract: Microarray platforms for performing one-color and two color analyses using a single platform are provided. Methods of using the microarray platforms and analyzing data obtained from such microarrays are also provided.

Abstract: Methods and compositions for generating pluralities of ribonucleic acids are provided. In the subject methods, an array is employed as a template in an in vitro transcription reaction. Also provided are the arrays employed in the subject methods and kits for practicing the subject methods. The ribonucleic acid pluralities produced by the subject methods find use in a variety of different applications, including differential gene expression analysis and gene-silencing applications.

Abstract: Methods and systems for identifying and selecting nucleic acid probes for detecting a target with a nucleic acid probe array or microarray, comprising selecting a plurality of candidate probes, forming a plurality of clusters from the plurality of candidate probes according to hybridization characteristics of the candidate probes, forming at least one SuperCluster from the clusters; and selecting at least one probe from each SuperCluster for the probe array.

Abstract: Methods are disclosed for selecting a combination of nucleic acid sample pairs for evaluating the ability of an oligonucleotide probe to measure differential expression of genes. Differential gene expression experiments are conducted using (i) nucleic acid sample pairs and (ii) nucleic acid probes immobilized on a substrate, the probes representing a set of genes. The number of genes in the set is a portion of an expected number of genes in a sample. A nucleic acid sample pair combination is selected based on the members of the combination having a maximized number of genes from the set of genes that exhibit differential expression and a minimized number of the genes that do not exhibit differential expression.