Abstract: Provided herein are collections of matched biological reagents selected from a larger collection of biological reagents, wherein the collection of matched biological reagents relate to a biological element. Also provided are methods for selling an isolated biomolecule or biological research reagent in a collection of matched biological reagents, and methods for selecting an isolated biomolecule or biological research reagent from a collection of biological reagents.

Abstract: Provided herein are collections of matched biological reagents selected from a larger collection of biological reagents, wherein the collection of matched biological reagents relate to a biological element. Also provided are methods for selling an isolated biomolecule or biological research reagent in a collection of matched biological reagents, and methods for selecting an isolated biomolecule or biological research reagent from a collection of biological reagents.

Abstract: The present invention provides compositions and methods for identifying molecules in samples that bind to molecules associated with pathogenic agents (e.g., infectious agents). In certain aspects, the invention may be used to identify individuals that have been exposed to one or more pathogenic agent or have generated antibodies in response to one or more pathogenic agent. In other aspects, the invention is directed to the identification of molecules of one or more pathogenic agent that may be used to generate immune responses in other individuals.

Abstract: Provided herein are novel panels of biomarkers for the diagnosis of autoimmune diseases, and methods and kits for detecting these biomarkers in samples of individuals suspected of having an autoimmune disease. Also provided are methods of monitoring the progression of an autoimmune disease and methods of monitoring the efficacy and side effects of a treatment for an autoimmune disease.

Abstract: The present invention provides human protein arrays that include at least 1000 human proteins. In another embodiment, the present invention provides a method for identifying a substrate of an enzyme, comprising contacting the enzyme with a positionally addressable array comprising at least 100 proteins immobilized on functionalized glass surface, and identifying a protein on the positionally addressable array that is bound and/or modified by the enzyme, wherein a binding or modifying of the protein by the enzyme indicates that the protein is a substrate for the enzyme. In additional embodiments, provided herein are methods for making an array of at least 1000 human proteins under non-denaturing conditions, including human proteins that are difficult to express and/or difficult to isolate in a non-denatured state.

Abstract: The present application relates to methods for providing a protein microarray product and related products and services to a customer, methods, kits, and systems for labeling a probe for a protein microarray, and methods for determining protein concentrations using a protein microarray. The methods for providing a protein microarray can include, in certain aspects, a computer function for performing some of the steps of the methods. Methods and kits for labeling a probe can include a control array that includes a molecule that binds to a label of a probe.

Abstract: The present invention relates to methods of conducting assays for enzymatic activity on microarrays useful for the large-scale study of protein function, screening assays, and high-throughput analysis of enzymatic reactions. The invention relates to methods of using protein chips to assay the presence, amount, activity and/or function of enzymes present in a protein sample on a protein chip. In particular, the methods of the invention relate to conducting enzymatic assays using a microarray wherein a protein and a substance are immobilized on the surface of a solid support and wherein the protein and the substance are in proximity to each other sufficient for the occurrence of an enzymatic reaction between the substance and the protein. The invention also relates to microarrays that have an enzyme and a substrate immobilized on their surface wherein the enzyme and the substrate are in proximity to each other sufficient for the occurrence of an enzymatic reaction between the enzyme and the substrate.

Abstract: The present invention provides compositions and methods for identifying molecules in samples that bind to molecules associated with pathogenic agents (e.g., infectious agents). In certain aspects, the invention may be used to identify individuals that have been exposed to one or more pathogenic agent or have generated antibodies in response to one or more pathogenic agent. In other aspects, the invention is directed to the identification of molecules of one or more pathogenic agent that may be used to generate immune responses in other individuals.

Abstract: Provided herein are novel panels of biomarkers for the diagnosis of autoimmune diseases, and methods and kits for detecting these biomarkers in samples of individuals suspected of having an autoimmune disease. Also provided are methods of monitoring the progression of an autoimmune disease and methods of monitoring the efficacy and side effects of a treatment for an autoimmune disease.

Abstract: The present invention provides human protein arrays that include at least 1000 human proteins. In another embodiment, the present invention provides a method for identifying a substrate of an enzyme, comprising contacting the enzyme with a positionally addressable array comprising at least 100 proteins immobilized on functionalized glass surface, and identifying a protein on the positionally addressable array that is bound and/or modified by the enzyme, wherein a binding or modifying of the protein by the enzyme indicates that the protein is a substrate for the enzyme. In additional embodiments, provided herein are methods for making an array of at least 1000 human proteins under non-denaturing conditions, including human proteins that are difficult to express and/or difficult to isolate in a non-denatured state.

Abstract: Disclosed are compositions and methods for detecting small quantities of analytes such as proteins and peptides. The method involves associating a primer with an analyte and subsequently using the primer to mediate rolling circle replication of a circular DNA molecule. Amplification of the DNA circle is dependent on the presence of the primer. Thus, the disclosed method produces an amplified signal, via rolling circle amplification, from any analyte of interest. The amplified DNA remains associated with the analyte, via the primer, and so allows spatial detection of the analyte. The disclosed method can be used to detect and analyze proteins and peptides. Multiple proteins can be analyzed using microarrays to which the various proteins are immobilized. A rolling circle replication primer is then associated with the various proteins using a conjugate of the primer and a molecule that specifically binds the proteins to be detectable.

Abstract: It has been determined Cortactin interacts with an ARG/ABL protein kinase. Thus, provided herein are compositions, kits and assays containing reagents directed to Cortactin and an ARG/ABL protein kinase.

Abstract: The present application relates to methods for providing a protein microarray product and related products and services to a customer, methods, kits, and systems for labeling a probe for a protein microarray, and methods for determining protein concentrations using a protein microarray. The methods for providing a protein micorarray can include, in certain aspects, a computer function for performing some of the steps of the methods. Methods and kits for labeling a probe can include a control array that includes a molecule that binds to a label of a probe.

Abstract: Provided herein are collections of matched biological reagents selected from a larger collection of biological reagents, wherein the collection of matched biological reagents relate to a biological element. Also provided are methods for selling an isolated biomolecule or biological research reagent in a collection of matched biological reagents, and methods for selecting an isolated biomolecule or biological research reagent from a collection of biological reagents.

Abstract: Disclosed are compositions and methods for detecting small quantities of analytes such as proteins and peptides. The method involves associating a primer with an analyte and subsequently using the primer to mediate rolling circle replication of a circular DNA molecule. Amplification of the DNA circle is dependent on the presence of the primer. Thus, the disclosed method produces an amplified signal, via rolling circle amplification, from any analyte of interest. The amplified DNA remains associated with the analyte, via the primer, and so allows spatial detection of the analyte. The disclosed method can be used to detect and analyze proteins and peptides. Multiple proteins can be analyzed using microarrays to which the various proteins are immobilized. A rolling circle replication primer is then associated with the various proteins using a conjugate of the primer and a molecule that specifically binds the proteins to be detectable.

Abstract: The present invention relates to methods of conducting assays for enzymatic activity on microarrays useful for the large-scale study of protein function, screening assays, and high-throughput analysis of enzymatic reactions. The invention relates to methods of using protein chips to assay the presence, amount, activity and/or function of enzymes present in a protein sample on a protein chip. In particular, the methods of the invention relate to conducting enzymatic assays using a microarray wherein a protein and a substance are immobilized on the surface of a solid support and wherein the protein and the substance are in proximity to each other sufficient for the occurrence of an enzymatic reaction between the substance and the protein. The invention also relates to microarrays that have an enzyme and a substrate immobilized on their surface wherein the enzyme and the substrate are in proximity to each other sufficient for the occurrence of an enzymatic reaction between the enzyme and the substrate.

Abstract: The present invention relates to methods of conducting assays for enzymatic activity on microarrays useful for the large-scale study of protein function, screening assays, and high-throughput analysis of enzymatic reactions. The invention relates to methods of using protein chips to assay the presence, amount, activity and/or function of enzymes present in a protein sample on a protein chip. In particular, the methods of the invention relate to conducting enzymatic assays using a microarray wherein a protein and a substance are immobilized on the surface of a solid support and wherein the protein and the substance are in proximity to each other sufficient for the occurrence of an enzymatic reaction between the substance and the protein. The invention also relates to microarrays that have an enzyme and a substrate immobilized on their surface wherein the enzyme and the substrate are in proximity to each other sufficient for the occurrence of an enzymatic reaction between the enzyme and the substrate.

Abstract: A prerequisite of proteomics is the ability to quantify many selected proteins simultaneously. Fluorescent sandwich immunoassays on microarrays hold appeal for such studies, since equipment and antibodies are readily available, and assays are simple, scalable and reproducible. To attain adequate sensitivity and specificity, however, a general method of immunoassay amplification is required. Coupling of isothermal rolling circle amplification (RCA) to universal antibodies can be used for this purpose: RCA on a synthetic DNA circle is initiated by a complementary oligonucleotide attached to an anti-biotin antibody; single-stranded RCA product remains attached to the antibody, and is detected by hybridization of complementary, fluorescent oligonucleotides. 51 cytokines were measured simultaneously on microarrays with signal amplification by RCA with high specificity, femtomolar sensitivity and 4 log quantitative range.

Abstract: Human extracellular ribonucleases (RNases) are widely distributed in various organs and body fluids and together with other members of the mammalian RNase A superfamily. In addition to their RNase activity, several RNases have been shown to have special biological actions, i.e., antitumor, antiviral and angiogenic properties. However, the molecular mechanisms of such activities are unclear. Using protein microarrays amplified rolling circle amplification (RCA), we investigated the effects of EDN (Rnase 2), ECP (Rnase 3) and RNase 1 on leukocytes cytokine production. We measured the levels of 78 different cytokines and growth factors in culture supernatants to determine the cytokine profiles of cells treated with different combinations of RNases and RNase inhibitors.

Abstract: Disclosed are compositions and methods for detecting small quantities of analytes such as proteins and peptides. The method involves associating a primer with an analyte and subsequently using the primer to mediate rolling circle replication of a circular DNA molecule. Amplification of the DNA circle is dependent on the presence of the primer. Thus, the disclosed method produces an amplified signal, via rolling circle amplification, from any analyte of interest. The amplified DNA remains associated with the analyte, via the primer, and so allows spatial detection of the analyte. The disclosed method can be used to detect and analyze proteins and peptides. Multiple proteins can be analyzed using microarrays to which the various proteins are immobilized. A rolling circle replication primer is then associated with the various proteins using a conjugate of the primer and a molecule that specifically binds the proteins to be detectable.