Abstract: Data extracted from fluorosphore responses of fluorophore labeled bases in genetic material used in sequencing of unknown fragments from a defined set of for example a model system are converted into a class of block codes that are then employed in a computer-based process to compare and correct preliminary calls of calls of the categorically known genetic material. In a specific embodiment, the Reed-Solomon codes are employed to identify one or more errors as may occur in a finite block of codes. The methodology is also useful to identify elements of a real system containing known elements in the form of a tag. Reed-Solomon sensors may be employed with and in addition to other types of genome sensors.

Abstract: Methods for linearly amplifying mRNA to produce antisense RNA are provided. In the subject methods, mRNA is converted to double-stranded cDNA using a promoter-primer having a poly-dT primer site linked to a promoter sequence so that the resulting double-stranded cDNA is recognized by an RNA polymerase. The resultant double-stranded cDNA is then transcribed into antisense RNA in the presence of a reverse transcriptase that is rendered incapable of RNA-dependent DNA polymerase activity during this transcription step. The subject methods find use a variety of different applications in which the preparation of linearly amplified amounts of antisense RNA is desired. Also provided are kits for practicing the subject methods.

Abstract: Data extracted from fluorosphore responses of fluorophore labeled bases in genetic material used in sequencing of unknown fragments from a defined set of for example a model system are converted into a class of block codes that are then employed in a computer-based process to compare and correct preliminary calls of calls of the categorically known genetic material. In a specific embodiment, the Reed-Solomon codes are employed to identify one or more errors as may occur in a finite block of codes. The methodology is also useful to identify elements of a real system containing known elements in the form of a tag. Reed-Solomon sensors may be employed with and in addition to other types of genome sensors.

Abstract: Methods and kits for labeling nucleic acids are provided. In the subject methods, an oligonucleotide tagged nucleic acid comprising an oligonucleotide tag is first generated. The oligonucleotide tagged nucleic acid is then contacted under hybridization conditions with a labeled oligonucleotide complementary to the oligonucleotide tag, yielding a labeled nucleic acid. The kits of the subject invention at least include a primer for use in enzymatically generating an oligonucleotide tagged target nucleic acid, where the primer generally at least includes an oligo dT region and the oligonucleotide tag, and a labeled oligonucleotide complementary to the oligonucleotide tag. The subject methods and kits find use in a variety of applications, and are particularly suited for use in gene expression analysis applications.

Abstract: Methods of identifying a sequence of a nucleic acid that is suitable for use as a surface immobilized probe for two or more mRNA transcripts encoded by the same gene are provided. In practicing the subject methods, a consensus region for the two or more transcripts is first identified, and this identified consensus region is then employed to identify the suitable nucleic acid sequence, e.g., by using a probe design protocol. The subject invention also includes algorithms for performing the subject methods recorded on a computer readable medium, as well as computational analysis systems that include the same. Also provided are nucleic acid arrays produced with probes having sequences identified by the subject methods, as well as methods for using the same.

Abstract: A polynucleotide array, and methods of making and using such arrays. The array may include a first set of multiple features each of which has first polynucleotide molecules of at least 400 nucleotides in length, and a second set of features each of which has second polynucleotide molecules of no more than 100 nucleotides in length. The second set of features can be used as control features, or to replace failed sequences in an enzymatic amplification to produce first polynucleotides, or to detect polymorphisms or splice variants which may not be detected by a particular first polynucleotide.

Abstract: Methods for linearly amplifying mRNA to produce antisense RNA are provided. In the subject methods, mRNA is converted to double-stranded cDNA using a promoter-primer having a poly-dT primer site linked to a promoter sequence so that the resulting double-stranded cDNA is recognized by an RNA polymerase. The resultant double-stranded cDNA is then transcribed into antisense RNA in the presence of a reverse transcriptase that is rendered incapable of RNA-dependent DNA polymerase activity during this transcription step. The subject methods find use a variety of different applications in which the preparation of linearly amplified amounts of antisense RNA is desired. Also provided are kits for practicing the subject methods.

Abstract: A buffer composition, method and kit for hybridizing microarrays of nucleic acids bound to an adsorbed polymer surface of a siliceous substrate provide an envelope of conditions to hybridize nucleic acid targets, while preserving theintactness of the adsorbed polymer surface of the array. The buffer composition comprises a non-chelating buffering agent, a pH within a range of pH 6.4 and 7.5, a monovalent cation having a monovalent cation concentration that ranges from about 0.01 M to about 2.0 M, and optionally relatively lower concentrations of a chelating agent and an ionic surfactant. The total cation concentration of the buffer composition ranges from about 0.02 M to about 2.0 M. The method comprises incubating the targets with the microarray in the buffer composition at a temperature between about 55° C. and 70° C.

Abstract: Methods of identifying a sequence of a probe, e.g., a biopolymeric probe, such as a nucleic acid, that is suitable for use as a surface immobilized probe for a target molecule of interest, e.g., a target nucleic acid, are provided. A feature of the subject methods is that a set of computationally determined initial candidate sequences are empirically evaluated to obtain functional data that is then employed to identify one or more clusters of candidate probe sequences from the initial set such that all candidate probe sequences within each identified cluster exhibitsubstantially the same performance under a plurality of different experiments, specifically a plurality of differential gene expression experiments. A candidate probe from the cluster that exhibits the best performance across the plurality of experimental sets is then selected as the optimum candidate probe, e.g., based on one or more performance metrics.

Abstract: Methods of identifying a sequence of a nucleic acid that is suitable for use as a surface immobilized probe for two or more mRNA transcripts encoded by the same gene are provided. In practicing the subject methods, a consensus region for the two or more transcripts is first identified, and this identified consensus region is then employed to identify the suitable nucleic acid sequence, e.g., by using a probe design protocol. The subject invention also includes algorithms for performing the subject methods recorded on a computer readable medium, as well as computational analysis systems that include the same. Also provided are nucleic acid arrays produced with probes having sequences identified by the subject methods, as well as methods for using the same.

Abstract: Methods for evaluating whether a sample of at least one detectably-labeled target biomolecule is suitable for use in an array based assay are provided. The subject methods include: (1) providing a substrate having an evaluation array thereon; (2) contacting the evaluation array with the sample; (3) detecting any resultant target biomolecules to obtain signal data; and (4) processing the signal data to evaluate whether the sample is suitable for use in a biopolymeric array assay. Many embodiments of the subject methods include using a volume of sample that does not exceed about 5 &mgr;l and/or incubating the sample with the array for a period of time that does not exceed about 4 hours. Also provided are methods of performing array based assays that include the subject evaluation methods, and kits for practicing the subject methods.

Abstract: Methods are disclosed for predicting the potential of a hybridization oligonucleotide of length greater than about 20 nucleotides to hybridize to a target nucleotide sequence. The method involves evaluating predictor oligonucleotides based on one or more parameters. A subset of oligonucleotides within the predetermined number of predictor oligonucleotides is selected based on an examination of the parameter and application of a rule that rejects some of the oligonucleotides identified above. Oligonucleotides are identified in the selected subset, viewed according to order of position along the nucleotide sequence, that are in clusters along a region of the nucleotide sequence. The clusters are ranked in order of number of oligonucleotides. A hybridization oligonucleotide is selected for each cluster, in descending order of cluster rank. The selected hybridization oligonucleotide has as its central nucleotide the central nucleotide of a region of the nucleotide sequence that corresponds to the cluster.

Abstract: Methods and kits for labeling nucleic acids are provided. In the subject methods, an oligonucleotide tagged nucleic acid comprising an oligonucleotide tag is first generated. The oligonucleotide tagged nucleic acid is then contacted under hybridization conditions with a labeled oligonucleotide complementary to the oligonucleotide tag, yielding a labeled nucleic acid. The kits of the subject invention at least include a primer for use in enzymatically generating an oligonucleotide tagged target nucleic acid, where the primer generally at least includes an oligo dT region and the oligonucleotide tag, and a labeled oligonucleotide complementary to the oligonucleotide tag. The subject methods and kits find use in a variety of applications, and are particularly suited for use in gene expression analysis applications.

Abstract: A method and system for normalizing two or more molecular array data sets. Input molecular array data sets are separately globally normalized by, for example, dividing the feature-signal magnitudes of each data set by the geometric mean of the feature-signal magnitudes of the data set. The globally normalized feature signal magnitudes within each data set are ranked in ascending order. A numeric function is created that relates feature-signal magnitudes of the data sets. Only a subset of the features, obtained by selecting features that are similarly ranked in the separate feature-signal-magnitude rankings for the data sets, is used to construct the numeric function. The numeric function is smoothed by one of many possible different smoothing procedures.

Abstract: A method and system for normalizing two or more molecular array data sets. Input molecular array data sets are separately globally normalized by, for example, dividing the feature-signal magnitudes of each data set by the geometric mean of the feature-signal magnitudes of the data set. The globally normalized feature signal magnitudes within each data set are ranked in ascending order. A numeric function is created that relates feature-signal magnitudes of the data sets. Only a subset of the features, obtained by selecting features that are similarly ranked in the separate feature-signal-magnitude rankings for the data sets, is used to construct the numeric function. The numeric function is smoothed by one of many possible different smoothing procedures.

Abstract: Methods and kits for labeling nucleic acids are provided. In the subject methods, an oligonucleotide tagged nucleic acid comprising an oligonucleotide tag is first generated. The oligonucleotide tagged nucleic acid is then contacted under hybridization conditions with a labeled oligonucleotide complementary to the oligonucleotide tag, yielding a labeled nucleic acid. The kits of the subject invention at least include a primer for use in enzymatically generating an oligonucleotide tagged target nucleic acid, where the primer generally at least includes an oligo dT region and the oligonucleotide tag, and a labeled oligonucleotide complementary to the oligonucleotide tag. The subject methods and kits find use in a variety of applications, and are particularly suited for use in gene expression analysis applications.

Abstract: Methods are disclosed for predicting the potential of an oligonucleotide to hybridize to a target nucleotide sequence. A predetermined number of unique oligonucleotides is identified. The unique oligonucleotides are chosen to sample the entire length of a nucleotide sequence that is hybridizable with the target nucleotide sequence. At least one parameter that is independently predictive of the ability of each of the oligonucleotides of the set to hybridize to the target nucleotide sequence is determined and evaluated for each of the above oligonucleotides. A subset of oligonucleotides within the predetermined number of unique oligonucleotides is identified based on the evaluation of the parameter. Oligonucleotides in the subset are identified that are clustered along a region of the nucleotide sequence that is hybridizable to the target nucleotide sequence. The method may be carried out with the aid of a computer.

Abstract: A buffer composition, method and kit for hybridizing microarrays of nucleic acids bound to an adsorbed polymer surface of a siliceous substrate provide an envelope of conditions to hybridize nucleic acid targets, while preserving the intactness of the adsorbed polymer surface of the array. The buffer composition comprises a non-chelating buffering agent, a pH within a range of pH 6.4 and 7.5, a monovalent cation having a monovalent cation concentration that ranges from about 0.01 M to about 2.0 M, and optionally relatively lower concentrations of a chelating agent and an ionic surfactant. The total cation concentration of the buffer composition ranges from about 0.02 M to about 2.0 M. The method comprises incubating the targets with the microarray in the buffer composition at a temperature between about 55° C. and 70° C.

Abstract: A polynucleotide array, and methods of making and using such arrays. The array may include a first set of multiple features each of which has first polynucleotide molecules of at least 400 nucleotides in length, and a second set of features each of which has second polynucleotide molecules of no more than 100 nucleotides in length. The second set of features can be used as control features, or to replace failed sequences in an enzymatic amplification to produce first polynucleotides, or to detect polymorphisms or splice variants which may not be detected by a particular first polynucleotide.

Abstract: Methods and kits for labeling nucleic acids are provided. In the subject methods, an oligonucleotide tagged nucleic acid comprising an oligonucleotide tag is first generated. The oligonucleotide tagged nucleic acid is then contacted under hybridization conditions with a labeled oligonucleotide complementary to the oligonucleotide tag, yielding a labeled nucleic acid. The kits of the subject invention at least include a primer for use in enzymatically generating an oligonucleotide tagged target nucleic acid, where the primer generally at least includes an oligo dT region and the oligonucleotide tag, and a labeled oligonucleotide complementary to the oligonucleotide tag. The subject methods and kits find use in a variety of applications, and are particularly suited for use in gene expression analysis applications.