Abstract: Methods and compositions for generating mixtures of product molecules from an initial chemical array are provided. In the subject methods, a chemical array of surface immobilized first moieties is subjected to cleavage conditions such that a composition of solution phase first moieties is produced. The resultant composition of solution phase first moieties is then contacted with one or more reactants to produce a mixture of product molecules that are different from the first moieties. Also provided are the arrays employed in the subject methods and kits for practicing the subject methods.

Abstract: Methods, systems and computer readable media for checking label integrity of labeled biopolymers in a single sample assayed by chemical array analysis. At least first and second labels are incorporated into biopolymers in the single sample to produce a multi-labeled, single sample. The multi-labeled, single sample is hybridized with probes on a chemical array, and signal values are read from probes on the chemical array bound to a set of biopolymer sequences labeled with the at least first and second labels. First-labeled signal values from a probe, having the first label incorporated therein, are compared with second-labeled signal values from the probe bound to biopolymer having the second label incorporated therein.

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: Methods and compositions for producing labeled probe nucleic acids from genomic nucleic acid template are provided. In the subject methods, a conserved coding consensus region primer is employed to enzymatically generate a select set of labeled probe nucleic acids corresponding to coding regions of genes from a genomic template via a primer extension protocol. The subject methods find use in a variety of different applications, and are particularly suited for use in the preparation of labeled probe nucleic acids for use in array based comparative genomic hybridization applications. Also provided are kits for use in practicing the subject methods.

Abstract: Methods and compositions for determining cytotoxicity of a transfection agent are provided. In one aspect, a cell is contacted with a transfection agent. Following contact, a cytotoxic marker profile of the cell is evaluated to determine whether the transfection agent has mediated a cytotoxic response in the cell. Also provided are compositions and reagents, and kits for practicing the subject methods. The subject methods and compositions find use in a variety of different applications.

Abstract: Methods and compositions for determining cytotoxicity of a transfection agent are provided. In one aspect, a cell is contacted with a transfection agent. Following contact, a cytotoxic marker profile of the cell is evaluated to determine whether the transfection agent has mediated a cytotoxic response in the cell. Also provided are compositions and reagents, and kits for practicing the subject methods. The subject methods and compositions find use in a variety of different applications.

Abstract: The invention relates to methods and kits for quantification of amplified nucleic acids, such as genomic DNA. The methods and kits can be used to assess bias in an amplification procedure such as a whole genome amplification procedure. In one aspect, the method comprises performing an enzyme-based amplification procedure and validating the results of the procedure using a signal amplification method.

Abstract: Methods for producing linearly amplified amounts of (+) strand RNA from an initial mRNA source are provided. In the subject methods, an initial mRNA source, e.g., total RNA, is converted to double-stranded cDNA using a second strand cDNA promoter-primer having a promoter sequence recognized by an RNA polymerase located at its 5? end. The resultant double-stranded cDNA is then transcribed into (+) RNA. The subject methods find use in a variety of different applications in-which the preparation of linearly amplified amounts of (+) RNA is desired. Also provided are kits for practicing the subject methods.

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 compositions for producing a labeled population of nucleic acids for use in an array-based comparative genome hybridization (CGH) assay are provided. In general, the methods involve cleaving a genomic source to produce a sample containing nucleic acid fragments, and end-labeling the nucleic acid fragments to provide a population of nucleic acids having a terminal label. Kits and systems for use in practicing the subject methods are also provided.

Abstract: Methods for generating mixtures of nucleic acids, e.g., oligonucleotide primers, are provided. In the subject methods, an array is employed as template to generate mixtures of nucleic acids via a template driven primer extension reaction. In preferred embodiments, each probe on the array employed in the subject methods comprises a constant domain and a variable domain, where the constant domain is further characterized by having at least a recognition domain. Also provided are the arrays employed in the subject methods and kits for practicing the subject methods. The subject methods find use in a variety of applications, including the generation of target nucleic acids from an mRNA sample for use in hybridization assays, e.g., differential gene expression analyses.

Abstract: Methods and compositions for generating mixtures of product molecules from an initial chemical array are provided. In the subject methods, a chemical array of surface immobilized first moieties is subjected to cleavage conditions such that a composition of solution phase first moieties is produced. The resultant composition of solution phase first moieties is then contacted with one or more reactants to produce a mixture of product molecules that are different from the first moieties. Also provided are the arrays employed in the subject methods and kits for practicing the subject methods.

Abstract: Methods and compositions for linearly amplifying mRNA from small RNA samples to produce antisense RNA are provided In the subject methods, mRNA is converted to a transcription template product by using a promoter primer, where the resultant product at least includes a first strand cDNA template domain and a double-stranded RNA polymerase promoter. A feature of the subject methods is that the ratio of the promoter-primer to the input RNA is chosen to provide for a high yield of selective RNA product. Additional optional features include the use of a thermostabilizing agent, e.g., raffinose, trehalose, etc., in the reverse transcription step and/or the use of a polyalkylene oxide, e.g., a PEG, in the in vitro transcription step. Also provided are compositions and kits that find use in practicing the subject methods. The subject invention finds use a variety of different applications in which the preparation of linearly amplified amounts of cRNA is desired.

Abstract: Methods and compositions for performing template dependent nucleic acid primer extension reactions that produce a reduced complexity product are provided. In the subject methods, template RNA is contacted with a primer composition that includes both a universal, e.g., oligo dT, primer and at least one gene specific primer under template dependent primer extension reaction conditions, which step results in the production of a reduced complexity product as compared to the initial RNA template. The subject methods find use a variety of different applications, including the preparation of labeled nucleic acids, e.g., for use in differential gene expression analysis applications. Also provided are kits for practicing the subject methods.