4355 results about "Analyte" patented technology

A method of capturing analytes from a sample is provided. A first substrate including a sample is mounted on a first member of a sample handling device and mounting a second substrate including an array of capture probes on a second member of the sample handling device. A first reagent medium is applied to the first and / or second substrate and moving the first member and / or the second member to fluidically couple the sample and the array of capture probes via the first reagent medium. The sample and the array of capture probes are fluidically decoupled by moving the first member and / or the second member and a second reagent medium is applied to the first and / or second substrate and moving the first member and / or the second member to fluidically couple the sample and the array of capture probes via the second reagent medium. Related systems and apparatuses are also provided.

Provided herein are materials and methods for in situ labeling of a biological sample for use in spatial analysis of one or more analytes in the biological sample. In some aspects, in situ labeling of a biological sample includes labeling the biological sample with one or more spatial barcodes.

The present disclosure relates to materials and methods for spatially analyzing nucleic acids that have been fragmented with a transposase enzyme, alone or in combination with other types of analytes.

Provided herein are methods, compositions, and kits for the spatial analysis of target nucleic acids, or complements thereof, by their 5′ end.

The present disclosure relates to materials and methods for spatially analyzing nucleic acids that have been fragmented with a transposase enzyme, alone or in combination with other types of analytes.

Provided herein are methods of identifying abundance and location of an RNA in a biological sample using an adaptor sequence and a primer. Also disclosed herein are kits. compositions, and systems that are used to perform the methods.

Disclosed herein are methods of amplifying an analyte in a biological sample using a bridging oligonucleotide that hybridizes to a captured analyte. The methods disclosed herein include steps of (a) contacting a biological sample with a substrate having capture probes comprising a capture domain and a spatial barcode; (b) hybridizing the analyte to the capture domain; and (c) contacting the analyte to a bridging oligonucleotide comprising (i) a capture-probe-binding sequence, and (ii) an analyte-binding sequence; (d) extending the bridging oligonucleotide; and (e) determining (i) all or a part of the sequence of the analyte, or a complement thereof, and (ii) the spatial barcode, or a complement thereof, and using the determined sequence of (i) and (ii) to determine the location of the analyte in the biological sample.

The present disclosure relates to materials and methods for spatially analyzing nucleic acids that have been fragmented with a transposase enzyme, alone or in combination with other types of analytes.

The present disclosure provides methods and compositions for detecting and spatially locating analyte interactions and gene expression in a biological sample. For example, provided herein are methods of determining a location of at least one analyte in a biological sample using analyte-binding moieties, proximity ligation, and an array including capture probes.

The present disclosure relates to materials and methods for spatially analyzing nucleic acids that have been fragmented with a transposase enzyme, alone or in combination with other types of analytes.

Provided herein are methods and compositions disclosing an approach that combines single nuclear RNA-seq (snRNA-seq) with spatial transcriptomics. The methods include processing and analyzing multiple analytes in a biological sample, and utilizes multiple substrates, one having a spatial array having a plurality of capture probes, each having a capture domain and a spatial barcode. The methods can be used to detect location of both nucleic acid and protein analytes. The methods also include isolating cells and / or nuclei from a sample and determining analyte expression in the isolated cells and / or nuclei.

Provided herein are methods of determining a location of a biological analyte in a biological sample.

The present disclosure relates to materials and methods for spatially analyzing nucleic acids that have been fragmented with a transposase enzyme, alone or in combination with other types of analytes.

Provided herein are methods for preparing biological samples for spatial proteomic analysis, methods of determining a location of a protein analyte in a biological sample, and methods of determining a location of a protein analyte and a nucleic acid analyte in a biological sample.

Localized detection of RNA in a tissue sample that includes cells is accomplished on an array. The array include a number of features on a substrate. Each feature includes a different capture probe immobilized such that the capture probe has a free 3′ end. Each feature occupies a distinct position on the array and has an area of less than about 1 mm2. Each capture probe is a nucleic acid molecule, which includes a positional domain including a nucleotide sequence unique to a particular feature, and a capture domain including a nucleotide sequence complementary to the RNA to be detected. The capture domain can be at a position 3′ of the positional domain.

This disclosure relates to methods for spatial profiling of analytes present in a biological sample. Also provided are methods for using spatially barcoded substrates to detect a biological analyte in a cell culture, an organism, and organoid. Also provided are methods for using spatially barcoded substrates to detect the temporal profile of a biological analyte.

The present disclosure relates to materials and methods for spatially analyzing nucleic acids that have been fragmented with a transposase enzyme, alone or in combination with other types of analytes.

Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample using RNA-templated ligation.

Provided herein are methods, compositions, and kits for the spatial detection of analytes using ligation-based capture assays.

Localized detection of RNA in a tissue sample that includes cells is accomplished on an array. The array include a number of features on a substrate. Each feature includes a different capture probe immobilized such that the capture probe has a free 3′ end. Each feature occupies a distinct position on the array and has an area of less than about 1 mm2. Each capture probe is a nucleic acid molecule, which includes a positional domain including a nucleotide sequence unique to a particular feature, and a capture domain including a nucleotide sequence complementary to the RNA to be detected. The capture domain can be at a position 3′ of the positional domain.

Provided herein are methods using an anisotropic structure within or in proximity to a biological sample. Such methods can include identifying a location of an analyte in a biological sample or reducing mislocalization of an analyte in a biological sample.

Provided herein are methods, compositions, and kits for reducing mislocalization of analytes hybridized to an array on a second substrate from a biological sample mounted on a first substrate in the context of an array-based spatial assay. The methods, compositions, and kits include application of a gel composition to the first substrate and / or the second substrate to reduce mislocalization of analytes.

Provided herein are methods of analyzing an analyte in a fixed biological sample on a first substrate that has been stored for a long period of time, the method comprising: (a) hybridizing a first probe and a second probe to the analyte of the fixed biological sample; (b) coupling the first probe and the second probe, thereby generating a connected probe; (c) aligning the first substrate with a second substrate comprising an array, wherein the array comprises a plurality of capture probes, wherein a capture probe of the plurality of capture probes comprises: (i) a spatial barcode and (ii) a capture domain; (d) when the biological sample is aligned with at least a portion of the array, (i) releasing the connected probe from the analyte and (ii) migrating the connected probe from the biological sample to the array; and (e) hybridizing the connected probe to the capture domain.

Provided herein are methods, compositions, and systems for improved in situ detection of analytes and spatial analysis using, e.g., a sequencing readout.

The present disclosure provides electrophoretic systems, methods and compositions for spatial analysis, which can serve to magnify or demagnify spatial resolution of analytes of interest that are captured using electrophoresis. Some implementations can use a diverging or converging electric field in an electrophoretic capture system. Such a divergent or convergent electric field, as opposed to a parallel electric field, can be generated by, for example, utilizing different sizes of electrodes associated with or imbedded in substrates. Also provided herein are electrophoretic systems, methods and compositions for spatial analysis, which can serve to selectively migrate one or more analytes from a region of interest in the biological sample for capture using electrophoresis.

The present disclosure relates to materials and methods for spatially analyzing nucleic acids that have been fragmented with a transposase enzyme, alone or in combination with other types of analytes.

Provided herein are methods of determining a location of a biological analyte in a biological sample.