Provided herein are colocalization-by-linkage assay (CLA) compositions and methods for multiplexed analysis of an analyte or analytes. The CLA compositions and methods, as described herein, are engineered to detect multiple analytes using multiple detection reagents coupled to a single support. Readout or detection sensitivity is achieved through the use of release-dependent transduction (RDT) or displacer-dependent transduction. Further multiplexing can also be achieved through the use of barcoded elements used in the capture and detection of an analytes.

Compositions and methods for identifying antigen-specific T cells, including determining paired T cell receptor sequences for a specific antigen, are described. Compositions and methods for identifying neoantigen-specific T cells are also described. Microfluidic devices useful for identifying antigen-specific T cells, and methods of using the same, are also described.

Provided herein are methods for simultaneous spatio-temporal measurement of gene expression and cellular activity.

The invention(s) cover a composition, where units of the composition are configured to interact with each other (e.g., as neighbors) in order enable decoding of positions of captured target material relative to neighboring units of the composition. In embodiments, the composition includes: a body; and a set of molecules coupled to the body, the set of molecules comprising a first subset and a second subset, wherein the first subset is structured for target analyte capture, and wherein the second subset is structured for interactions with one or more neighboring objects. The invention(s) also cover systems incorporating one or more units of the composition and methods implementing units of the composition.

The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.

A cell analysis device includes a determination target identifier extraction portion configured to extract a determination target identifier that is information indicating an identification substance associated with a determination target cell that is a cell of a determination target from a table indicating a corresponding relationship between the cell and the identification substance for each compartment with respect to compartments flowing along a flow path including the cell and the identification substance that is a substance associated with the cell, an identifier acquisition portion configured to acquire the identifier that is the information for identifying the identification substance included in the compartments flowing along the flow path, a determination portion configured to determine a compartment including the determination target cell among the compartments flowing along the flow path on the basis of the identifier acquired by the identifier acquisition portion and the determination target identifier extracted by the determination target identifier extraction portion, and an output portion configured to output a determination result of the determination portion.

Methods and reagents for multiplex detection of antibodies are disclosed. In particular, the invention relates to multiplex detection of antibodies using antigen-DNA and antibody-binding agent-DNA conjugates carrying DNA barcodes for identifying and quantitating disease-relevant antibody isotypes, such as those involved in allergic responses, autoimmune diseases, infections, and inflammation.

The present invention provides methods for signal amplification. The methods use DNA hybridization chain reaction to build labeled nanoscaffolds off of target analytes. The methods are reversible, as the detectable signal can be removed using DNA hybridization and hydrolysis.

Methods of detecting a target in a sample are provided. Kits for performing the methods described herein are also provided.

Disclosed herein, inter alia, are compositions and methods of use thereof for interrogating a cell.