Abstract: Disclosed herein are methods, compositions and kits for quantitating one or more specific nucleic acids within a plurality of nucleic acids. In some embodiments, a sequencing library is constructed from enriched probe extension products specific for the specific nucleic acids and sequenced. In some embodiments, the resulting reads are used for removing duplicate reads. In some embodiments, counting of verified probes is used to quantitate or determine the number of specific nucleic acid molecules in the starting nucleic acid sample.

Abstract: Described herein are methods, compositions, and kits for library quantitation and qualification. Some embodiments relate to a method of library quantitation. For example, the method may include providing DNA fragments, amplifying the DNA fragments by polymerase chain reaction (PCR) in the presence of primers each labeled with a fluorophore. In these instances, only a predetermined number of fluorophores are attached to each DNA fragment. The method may further include detecting a fluorescent signal produced by the amplified DNA fragments and calculating a number of the amplified DNA fragments based on the detected fluorescent signal.

Abstract: Described herein are methods, compositions and kits for identifying modifications that could lead to false positive detections in nucleic acid sequencing. In some embodiments, the methods, compositions and kits provided herein are useful for reducing potential of false positive detection of variants caused by errors during sample preparation or sequencing.

Abstract: The present invention provides methods, compositions and kits for detecting duplicate sequencing reads. In some embodiments, the duplicate sequencing reads are removed.

Abstract: The present invention provides methods, compositions and kits for detecting duplicate sequencing reads. In some embodiments, the duplicate sequencing reads are removed.

Abstract: Disclosed herein are methods, compositions and kits for quantitating one or more specific nucleic acids within a plurality of nucleic acids. In some embodiments, a sequencing library is constructed from enriched probe extension products specific for the specific nucleic acids and sequenced. In some embodiments, the resulting reads are used for removing duplicate reads. In some embodiments, counting of verified probes is used to quantitate or determine the number of specific nucleic acid molecules in the starting nucleic acid sample.

Abstract: The present invention provides methods, compositions and kits for detecting duplicate sequencing reads. In some embodiments, the duplicate sequencing reads are removed.

Abstract: Comparative genomic hybridization assays and compositions for use in practicing the same are provided. A characteristic of the subject comparative genomic hybridization assays is that solid support immobilized oligonucleotide feature elements, e.g., in the form of an array, are employed. Specifically, at least first and second nucleic acid populations prepared from genomic templates are contacted with a plurality of distinct oligonucleotide feature elements immobilized on a solid support surface and the binding of the at least first and second populations is then evaluated. Also provided are kits for use in practicing the subject methods.

Abstract: Comparative genomic hybridization assays and compositions for use in practicing the same are provided. A characteristic of the subject comparative genomic hybridization assays is that solid support immobilized oligonucleotide feature elements, e.g., in the form of an array, are employed. Specifically, at least first and second nucleic acid populations prepared from genomic templates are contacted with a plurality of distinct oligonucleotide feature elements immobilized on a solid support surface and the binding of the at least first and second populations is then evaluated. Also provided are kits for use in practicing the subject methods.

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: A method of testing multiple fluid samples with multiple biopolymer arrays. A cover is assembled to a contiguous substrate carrying on a first side, multiple arrays each with multiple regions of biopolymers linked to the substrate, such that the cover and the substrate together form a plurality of chambers each containing a biopolymer array and each being accessible through its own port. Multiple fluid samples are introduced into respective chambers through a port of each such that the fluid samples contact respective arrays. A binding pattern of the arrays is observed. An apparatus and kit useful in such methods, are also provided.

Abstract: Methods for detecting the integration of viral nucleic acids into a host cell, and methods for determining the locus of integration using microarrays are described. The methods can also be used in conjunction with viral vectors used in gene therapy.

Abstract: Methods and articles for analyzing nucleotide sequences of nucleic acid molecules, e.g., using multiple probes per spot of an array, are described. In some embodiments, the methods and articles can reduce the numbers of arrays necessary to probe regions of interest in a biological sample, and/or increase the resolution at which biological events are probed. In some cases, these methods exploit the vertical aspect of an array in order to decrease the number of arrays or spots required for an assay. These probes may be in the form of compound probes, which comprise at least first and second probes, including first and second nucleotide sequences capable of hybridizing to first and second target nucleotide sequences, respectively, in a nucleic acid molecule of interest.

Abstract: Methods and devices for producing a polymer at a location of a substrate are provided. In the subject methods, a fluid droplet containing a first monomer labeled with a first detectable label is deposited from a fluid deposition device onto a location of a substrate surface having a second monomer labeled with a second detectable label. The first and second detectable labels are then detected to determine any misalignment between the fluid deposition device and the location of the substrate surface during deposition. Also provided are algorithms that perform the subject methods, as well as fluid deposition devices that include the subject algorithms. The subject invention also includes arrays produced according to the subject methods and kits that include the subject arrays.

Abstract: A method of testing multiple fluid samples with multiple biopolymer arrays. A cover is assembled to a contiguous substrate carrying on a first side, multiple arrays each with multiple regions of biopolymers linked to the substrate, such that the cover and the substrate together form a plurality of chambers each containing a biopolymer array and each being accessible through its own port. Multiple fluid samples are introduced into respective chambers through a port of each such that the fluid samples contact respective arrays. A binding pattern of the arrays is observed. An apparatus and kit useful in such methods, are also provided.

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 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 for stripping and reusing arrays are disclosed. Also disclosed are reagents and kits comprising control target molecules for determining the efficacy of a stripping condition to which an array has been exposed.

Abstract: Methods and devices for detecting deposition unit misalignment, e.g., printhead misalignment, of an in situ polymeric, e.g., a nucleic acid, array synthesis device are provided. In accordance with the subject methods, at least one test probe feature is synthesized on a substrate using an in situ polymeric array, e.g., nucleic acid array or protein array, synthesis device. The at least one test probe feature is then contacted with at least two different distinguishably labeled targets, e.g., target nucleic acids. The binding of the targets to the at least one test probe feature is then evaluated to detect any misalignment, e.g., deposition unit or pulse jet misalignments, of the synthesis device. Also provided are substrates having at least one test probe feature and at least one polymeric array, as well as methods of using the substrates in array assays. Also included are kits for use in practicing the subject methods.

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.