Provided herein are methods and systems for sensitive and multiplexed in situ analysis of samples such as biological samples using cleavable hapten linked targeting agents and cleavable detectably-labeled hapten-binding agents. In particular, provided herein are methods for multiplexed single-cell in situ biomolecule profiling in samples, including fixed or fresh tissues, and also allows the investigation of the different cell compositions and their spatial organizations in intact tissues through consecutive cycles of probe hybridization, fluorescence imaging, and signal removal.

A method of identifying extant proteins, including (a) inputting to a computer processor: (i) a plurality of empirical binding profiles, individual empirical binding profiles including empirical binding outcomes for binding of an extant protein to a plurality of different affinity reagents, (ii) a plurality of candidate outcome profiles, individual candidate outcome profiles including binding outcomes for binding of a candidate protein to the plurality of different affinity reagents, and (iii) a plurality of pseudo outcome profiles, individual pseudo outcome profiles including a rearrangement of a candidate outcome profile; (b) performing a process in the computer processor to identify extant proteins based on the empirical binding profiles of the extant proteins and the plurality of candidate outcome profiles; and (c) performing a process in the computer processor to determine a false discovery statistic for the extant proteins based on the plurality of pseudo outcome profiles.

This application relates to a method for fabricating a biofunctionalized surface on a substrate, wherein the substrate comprises hydroxyl groups on the surface to be biofunctionalized, the method comprising: covalently attaching organosilane groups to less than all of the hydroxyl groups on the surface of the substrate; covalently attaching one or more biospecies to the surface of the substrate; and applying a lubricant to the substrate, wherein the biospecies comprises a biorecognition element that detects a target analyte in a sample. A biofunctionalized surface made therefrom and use thereof, such as for biosensing applications, are also disclosed.

The methods described herein provide a means of producing an array of spatially separated proteins. The method relies on covalently attaching each protein of the plurality of proteins to a structured nucleic acid particle (SNAP), and attaching the SNAPs to a solid support.

Compositions, methods and systems are provided for isolating nucleic acids. A polymerase-nucleic acid complex can be formed by mixing a polymerase enzyme comprising strand displacement activity and a mixture of double stranded nucleic acids. Nucleic acid synthesis can then be initiated by the polymerase enzyme to produce a nascent strand complementary to the first strand, thereby displacing a portion of the second strand. After halting or reducing the rate of nucleic acid synthesis, a hybridizing a hook oligonucleotide can be used hybridize to the nucleic acid through a capture region on the hook oligonucleotide that is complementary to the displaced portion of the second strand. The nucleic acid can then be isolated from the mixture of nucleic acids using the hook oligonucleotide.

A method for magnetic cellular manipulation may include contacting a composition with a biological sample to form a mixture. The composition may include a plurality of particles. Each particle in the plurality of particles may include a magnetic substrate. The magnetic substrate may be characterized by a magnetic susceptibility greater than zero. The composition may also include a chargeable silicon-containing compound. The chargeable silicon-containing compound may coat at least a portion of the magnetic substrate. The biological sample may include cells and/or cellular structures. The method may also include applying a magnetic field to the mixture to manipulate the composition.

Described herein are thermo-responsive microbead compositions, methods of making such microbead compositions, and method employing the microbeads to evaluate cellular responses elicited by mechanical force.

The present invention provides a method of making an assay device for conducting an assay to detect a concentration of an analyte in a sample fluid. The assay devices would typically have a substantially planar surface having a series of site specific immobilized calibration spot arrays containing pre-determined quantities of the analyte printed thereon. In addition, a series of site specific immobilized test spot arrays, including capture antibody for binding the analyte protein is printed on the assay device. The method involves first modifying the planar surface to provide hydrophobic binding sites, hydrophilic linking and covalent bonding sites. Then the method requires printing the series of site specific immobilized test spot arrays and the series of site specific immobilized calibration spot arrays on the substantially planar surface. Applying the sample fluid to the assay device is the next step followed by testing a sensitivity of the assay and modulating ratios of the hydrophobic, hydrophilic and covalent binding sites in order to optimize the sensitivity of the assay.

Described herein are systems and methods for detecting a target analyte in a sample with electrodes, comprising a linker and an antibody attached to the linker, and measuring an electrocatalytic signal changes generated by binding of an analyte in the sample to the antibody. Also disclosed herein are kits for electrochemical detection of protein analytes.

Disclosed is a method for measurement of an analyte in a microparticle-based analyte-specific binding assay, wherein the microparticles are coated with the first partner of a binding pair, the method involving mixing the coated microparticles, an analyte-specific binding agent conjugated to the second partner of the binding pair, and a sample suspected of containing or containing the analyte, wherein the second partner of the binding pair is bound to the analyte-specific binding agent via a linker having from 12 to 30 ethylene glycol units (PEG 12 to 30), thereby binding the analyte via the conjugated analyte-specific binding agent to the coated microparticles, separating the microparticles having the analyte bound via the binding pair and the analyte-specific binding agent from the mixture and measuring the analyte bound to the microparticles.