Abstract: Methods and systems for selecting a cell of interest based on immune cell data are disclosed. For example, a method may comprise obtaining a single cell or spatial dataset, wherein the single cell or spatial dataset comprises a dataset of immune cell receptors, antibodies, or fragments thereof from a sample; identifying a clonotype group in the single cell or spatial dataset; selecting a schema to visualize selected amino acids in the clonotype group based on positions or chemical identity of the selected amino acids; visualizing the selected amino acids in the clonotype group in a graphic representation according to the schema; and selecting a cell of interest from the clonotype group based on a pre-defined criterion using the graphic representation.

Abstract: An assembly includes a stage body, a cam plate disposed on the body, and a sample positioning plate having a sample positioning surface configured to receive a sample device. The surface has first, second, and third raised portions. The second raised portion is disposed between the first and third raised portions. The first, second, and third raised portions are configured to contact the sample device. The assembly includes a riser module disposed within the stage body. The riser module is coupled to the plate and the body. The assembly includes a lid configured to be coupled to the cam plate. The lid has a coupled configuration and an uncoupled configuration such that, when in the coupled configuration, a recess is formed by the lid and the plate. The assembly includes one or more light sources disposed in the cam plate that are configured to direct light within the recess.

Abstract: Provided herein are methods of detecting target nucleic acids and uses of the same.

Abstract: Provided herein are methods of determining a location of a target nucleic acid in a biological sample.

Abstract: Various embodiments of the present disclosure disclose a system for forming a sealed chamber for preparing samples therein. In particular, various embodiments present an assembly that includes a sample device and a lid for forming a sealed chamber that can be used for, among other things, incubating samples therein. When the lid engages with the sample device, a plurality of snap joint elements of the lid engage with a respective plurality of snap joint elements to form a seal between the lid and the sample device.

Abstract: The present disclosure relates in some aspects to methods and compositions for in situ analysis involving catalytic de-crosslinking of biological samples.

Abstract: The present disclosure provides systems and methods for making a hydrogel comprising a cell, cell nucleus, or one or more components derived from a cell or cell nucleus. A method for making a hydrogel may comprise providing a cell or cell nucleus, a first polymer, wherein the first polymer comprises a plurality of first crosslink precursors, each of the plurality of first crosslink precursors comprising an azide group; providing a second polymer, wherein the second polymer comprises a plurality of second crosslink precursors, each of the plurality of second crosslink precursors comprising an alkyne group; and crosslinking the first polymer and the second polymer via a reaction between a first section of the first crosslink precursors and a second section of the second crosslink precursors, thereby providing the hydrogel comprising the cell or cell nucleus.

Abstract: The present disclosure provides methods of generating supports (e.g., beads) comprising barcode molecules coupled thereto. A barcode molecule coupled to a support may comprise a barcode sequence and a functional sequence. A barcode molecule may be generated using two or more ligation reactions in a combinatorial fashion. A support comprising two or more different barcode molecules may be useful for analyzing or processing one or more analytes such as nucleic acid molecules, proteins, and/or perturbation agents.

Abstract: The present disclosure relates in some aspects to methods for analyzing antigen receptor transcripts in a biological sample. In some aspects, nucleic acid molecules are generated from V(D)J transcripts in situ in the biological sample to enrich molecules comprising V(D)J joins. In some aspects, the presence, amount, and/or identity of a plurality of V(D)J transcripts are analyzed in situ. Also provided are oligonucleotides, sets of oligonucleotides, compositions, and kits for use in accordance with the methods.

Abstract: The present disclosure relates in some aspects to methods and compositions for analyzing biological samples involving active stripping of detectably labeled probes from hybridization complexes such as rolling circle amplification products (RCPs). In some embodiments, the present application provides a method wherein double-stranded hybridized complexes are dissociated by DNA helicases. In some embodiments, single-stranded binding proteins facilitate the dissociation and prevent hybridization of the dissociated strands.

Abstract: The present disclosure relates to methods, compositions, systems, and kits for detecting and analyzing the glycosylation of healthy and diseased cells and protein-specific glycosylation patterns using single-cell profiling methodologies.

Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing.

Abstract: Provided herein are methods for capturing a connected probe and/or a capture handle sequence to a capture domain of a capture probe.

Abstract: The present invention is directed to methods, compositions and systems for analyzing sequence information while retaining structural and molecular context of that sequence information.

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

Abstract: The present disclosure relates in some aspects to methods of contacting a biological sample (e.g., fresh or frozen tissue sample) with peptide-loaded detection complexes. In some aspects, the peptide-loaded detection complexes comprise antigen presenting molecule monomers or multimers that bind to antigens, reporter oligonucleotides that correspond to the antigen/antigen presenting molecule combination. In some aspects, the peptide-loaded detection complexes are tetramers. In some aspects, the tetramers bound to T cell receptors of T cells may be detected in situ. In some aspects, the tetramers bound to TCRs may be detected on an in situ platform and/or using an array comprising spatially barcoded capture agents. In some embodiments, the method comprises contacting a plurality of peptide-loaded detection complexes to clonal populations of T cells comprising TCRs of different antigen specificities.

Abstract: Provided herein are methods, compositions, and kits for removing a portion of a sequence in a member of a nucleic acid library.

Abstract: A magnetic separator is disclosed. The magnetic separator comprises an array of magnets configured to interact with a tube holder plate, wherein the tube holder plate comprises an array of tubes. The magnetic separator comprises a raised frame extending around a periphery of the array of magnets such that the raised frame is configured to support the tube holder plate such that the array of tubes is suspended above the array of magnets.

Abstract: The present disclosure provides methods of processing or analyzing a sample. A method for processing a sample may comprise hybridizing a probe molecule to a target region of a nucleic acid molecule (e.g., a ribonucleic acid (RNA) molecule), barcoding the probe-nucleic acid molecule complex, and performing extension, denaturation, and amplification processes. A method for processing a sample may comprise hybridizing first and second probes to adjacent or non-adjacent target regions of a nucleic acid molecule (e.g., an RNA molecule), linking the first and second probes to provide a probe-linked nucleic acid molecule, and barcoding the probe-linked nucleic acid molecule. One or more processes of the methods described herein may be performed within a partition, such as a droplet or well. One or more processes of the methods described herein may be performed on a cell, such as a permeabilized cell.