Abstract: A method of processing a target RNA is provided. In certain embodiments, this method comprises: contacting the products of an RNA ligase-mediated ligation reaction with an CAS6 protein, wherein: (i) the RNA ligase-mediated ligation reaction comprises: a target RNA, an RNA ligase, and first and second adaptors that can ligate together to produce an adaptor dimer that contains a CRISPR stem loop; and (ii) the CAS6 protein recognizes the CRISPR stem loop; thereby preventing the adaptor dimer from being reverse transcribed.

Abstract: A method of processing a target RNA is provided. In certain embodiments, this method comprises: contacting the products of an RNA ligase-mediated ligation reaction with an CAS6 protein, wherein: (i) the RNA ligase-mediated ligation reaction comprises: a target RNA, an RNA ligase, and first and second adaptors that can ligate together to produce an adaptor dimer that contains a CRISPR stem loop; and (ii) the CAS6 protein recognizes the CRISPR stem loop; thereby preventing the adaptor dimer from being reverse transcribed.

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: The present invention provides polynucleotides and polypeptides (VECSM polynucleotides and polypeptides) that are differentially expressed in vascular endothelial cells. The invention further provides a variety of compositions, diagnostic, and therapeutic methods based on identification of these markers. In particular, the invention provides a targeting agent linked to a functional moiety, wherein the functional moiety can comprise any of a number of different agents, including imaging agents, cytotoxic agents, and stimulators or inhibitors of angiogenesis.

Abstract: The invention identifies genes whose expression is upregulated or downregulated following mechanical offloading in subjects with heart failure. The invention provides compositions comprising a targeting agent conjugated to a functional moiety, wherein the targeting agent selectively binds to a polypeptide encoded by one of these genes. The functional moiety can be an imaging agent, therapeutic agent, etc. The invention further provides methods for providing diagnostic or prognostic information related to heart failure involving detecting expression or activity of an expression product of one or more of the identified genes. The invention further provides diagnostic and therapeutic methods comprising detecting or administering an apelin peptide to a subject.

Abstract: Patient specific array-based assays are provided. A feature of the subject patient specific array-based assays is that they include a step of interrogating a set of array features that have been previously identified by a general array-based assay to be relevant to a specific disease and condition of the subject being assayed. Also provided are methods of producing the subject patient specific array-based assays, as well as compositions and kits for use in practicing the subject assays.

Abstract: The present invention provides systems and methods for determining the cell type composition of a mixed cell population. The invention provides systems and methods for identifying and defining pure cell type specific signatures. These pure cell type specific signatures may be used to determine the cell type composition of a mixed cell population. The systems and methods of the invention may be used for a variety of research and clinical purposes. For example, they may be used to detect the presence or absence of cells of particular types, and to determine whether variations in gene expression, e.g., between different samples, represent true changes in gene expression or differences in cell type composition of the samples.

Abstract: An apparatus and method for separating and identifying chemical moieties. The apparatus employs a microarray device coupled to a nanopore system. The apparatus both separates and identifies target molecules without the requirement of extraneous tags or fluorescent markers. Methods for using the apparatus are also disclosed.

Abstract: A method of using a chemical array unit having a chemical array with probes at multiple feature locations. A request for test may be read, which test uses a sub-array of the array. A pattern of the sub-array may be retrieved from a memory using the test request, which memory carries a pattern for the sub-array which is retrievable with the different test request. Also, a method of reading a chemical array unit which has been exposed to a sample, and feature locations of which have been rendered incapable of providing signal data representative of binding of a sample component. Further methods, apparatus, and computer program products are provided.

Abstract: An apparatus and method for separating and identifying chemical moieties. The apparatus employs a micro array device coupled to a detector such as a mass spectrometer system. The apparatus both separates and identifies target molecules without the requirement of extraneous tags or fluorescent markers. Methods for using the apparatus are also disclosed.

Abstract: Array-based clinical assays and compositions for use in practicing the same are provided. A feature of the subject array-based clinical assays is that they include a sample quality evaluation step that is independent from the clinical assay step of the assays, where the sample quality evaluation step may be performed in a number of different ways. Also provided are compositions, devices and 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: The invention provides novel methods for surface treatment of bioarrays to provide desirable substrate surface characteristics, and novel methods for fabrication of bioarrays. The present invention encompasses a process of contacting the surface of a substrate having biomolecules deposited thereupon with a basic, aqueous solution, followed by contacting the surface with a blocking agent that bonds preferentially to surface reactive moieties on the surface and reduces background signal and/or reduces the number of sites available for non-specific binding to occur. The invention also encompasses bioarrays fabricated using such process.

Abstract: Methods and devices for depositing a nucleic acid on a substrate surface are provided. In the subject methods, a thermal inkjet head loaded with nucleic acid fluid composition is positioned in opposing relationship to, e.g. over, a substrate surface. Actuation of the thermal inkjet results in the expulsion of volume of the nucleic acid composition onto the substrate surface. The subject methods and devices find use in a variety of applications, particularly in the preparation of nucleic acid arrays, and more particular arrays of oligonucleotides or polynucleotides, e.g. cDNAs.