Abstract: The present invention, among other things, provides technologies for detecting and/or quantifying nucleic acids in cells, tissues, organs or organisms. In some embodiments, through sequential barcoding, the present invention provides methods for high-throughput profiling of a large number of targets, such as transcripts and/or DNA loci.

Abstract: The present invention, among other things, provides technologies for detecting and/or quantifying nucleic acids in cells, tissues, organs or organisms. In some embodiments, through sequential barcoding, the present invention provides methods for high-throughput profiling of a large number of targets, such as transcripts and/or DNA loci.

Abstract: The present invention, among other things, provides technologies for detecting and/or quantifying nucleic acids in cells, tissues, organs, or organisms. Pre-designed barcodes are associated with specific molecular targets through sequential hybridization experiments. A pseudo-color based barcoding scheme is described that overcomes the limitations in the previous generation of the technology. The current method can be applied to both in vitro and in situ analysis.

Abstract: Disclosed herein include systems, methods, compositions, and kits for in situ readout of barcodes, such as DNA barcodes. Barcode constructs containing a promoter (e.g., a phage promoter) that is inactive in live cells can be integrated in the genomes of cells. Cells can be fixed, and phage RNA polymerase can be used for transcription of the barcode to RNA transcripts. The RNA transcripts can be detected using, for example, fluorescent imaging and used to determine barcode sequences.

Abstract: The present invention, among other things, provides technologies for detecting and/or quantifying nucleic acids in cells, tissues, organs, or organisms. Pre-designed barcodes are associated with specific molecular targets through sequential hybridization experiments. A pseudo-color based barcoding scheme is described that overcomes the limitations in the previous generation of the technology. The current method can be applied to both in vitro and in situ analysis.

Abstract: The present disclosure provides methods for encoding and decoding signals from barcodes in a plurality of molecular targets from images obtained from imaging based spatial genomics (ISG) experiments. This disclosure sets forth methods, in addition to use of the same, and other solutions to problems in the relevant field.

Abstract: The present invention, among other things, provides technologies for detecting and/or quantifying nucleic acids in cells, tissues, organs or organisms. In some embodiments, through sequential barcoding, the present invention provides methods for high-throughput profiling of a large number of targets, such as transcripts and/or DNA loci.

Abstract: Disclosed herein is a composition for nuclease treatment of hybridized probes in experiments to profile and analyze biological samples. Also disclosed herein, is a kit for nuclease treatment of hybridized probes in experiments to profile and analyze biological samples. Also disclosed herein, is a method for nuclease treatment of hybridized probes in experiments to profile and analyze biological samples.

Abstract: The present invention, among other things, provides technologies for detecting and/or quantifying nucleic acids in cells, tissues, organs or organisms. In some embodiments, through sequential barcoding, the present invention provides methods for high-throughput profiling of a large number of targets, such as transcripts and/or DNA loci.

Abstract: The present disclosure provides methods for analyzing genomic structures by diffraction limited locus imaging and nucleic acid block coding. The methods allow efficient and scalable imaging, which can be applied to multiplexed RNA/DNA fluorescence in situ hybridization (FISH).

Abstract: Disclosed herein are methods for generating an ratiometric symbol for sequential hybridization barcoding for multiplexed Fluorescence In Situ Hybridization (FISH). Also, the disclosure sets forth methods, in addition to using the same, and other solutions to problems in the relevant field.

Abstract: Disclosed herein are methods for generating a massive number of chemically ligateable probes for multiplexed Fluorescence In Situ Hybridization (FISH) using a hybrid-primer. Also, the disclosure sets forth methods, in addition to using the same, and other solutions to problems in the relevant field.

Abstract: Disclosed herein is a composition for linked amplification tethered with exponential radiance for signal amplification. Also disclosed herein, is a kit for linked amplification tethered with exponential radiance for signal amplification. Also disclosed herein, is a method linked amplification tethered with exponential radiance for signal amplification.

Abstract: Method for detecting and barcoding the molecular changes occurring in two or more samples upon exposure to different stimuli. This disclosure herein sets for methods that allow a targeted transcriptome-imaging approach that records both gene-expression and spatial context within microscale assemblies at a single-cell and molecule resolution on biological samples. This disclosure herein sets for methods that allows the application to a variety of biological samples for the study of cellular processes, growth, and interactions between biological samples.

Abstract: This disclosure herein sets forth embodiments for a method for mapping the spatial distribution of one or more cellular components or cellular interactions by using barcodes to identify a cell or cellular component in the one or more cells, localizing, detecting, and mapping the spatial distribution of the one or more cellular components. The disclosure herein sets forth method to allow the mapping of spatial distributions of cellular components both intracellularly or intercellularly.

Abstract: The present invention, among other things, provides technologies for detecting and/or quantifying nucleic acids in cells, tissues, organs or organisms. In some embodiments, through sequential barcoding, the present invention provides methods for high-throughput profiling of a large number of targets, such as transcripts and/or DNA loci.

Abstract: The present application describes compositions and methods for identifying and quantitating molecular targets within a cellular environment. Specifically, provided herein are compositions and methods for separately identifying and quantifying each of one or more molecular targets from a single cell. More specifically, provided herein are compositions and methods for separately identifying and quantifying the same molecular target from a single cell.

Abstract: The present invention, among other things, provides technologies for detecting and/or quantifying nucleic acids in cells, tissues, organs or organisms. In some embodiments, through sequential barcoding, the present invention provides methods for high-throughput profiling of a large number of targets, such as transcripts and/or DNA loci.

Abstract: A multi-channel line microscope for single molecule Fluorescence In Situ Hybridization (FISH) imaging of a sample. A microscope stage moves a sample across two or more reflected excitation lines positioned relative to each other so that each excitation line excites a spatially distinct horizontal line in the image plane of the sample. A sample is imaged by moving the microscope stage across two or more reflected excitation lines positioned relative to each other so that each excitation line excites a spatially distinct horizontal line in the image plane of the sample. The apparatus and methods of use are suitable for a broad range of applications.