Abstract: Compositions, methods, and kits for performing multiplexed, spatially resolved, or single-cell chromatin analysis are provided.

Abstract: Methods for strand-displacement amplification of a target nucleic acid have been developed. Compositions for use according to the methods are also provided. The methods typically include steps of removing, hybridizing and extending a selectively removable or digestible primer with a strand-displacing DNA polymerase once or more than once to provide a multiplicity of copies of the target nucleic acid. Methods for strand-displacement amplification of single or double-stranded target DNA molecules are provided. In some forms, when the methods include amplification of a double-stranded nucleic acid, the methods employ one or more adapter handles that perform the function of providing a removable region on a single strand of the ds target. Compositions and kits of oligonucleotide primers and double-stranded nucleic acid adapters including selectively removable regions are also provided for use in the described methods.

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. The nucleic acid molecule may be a nucleic acid molecule associated with CRISPR, (e.g., a guide RNA). 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 such as a guide 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.

Abstract: Provided herein are systems and methods for analyzing biomolecules (e.g., nucleic acid molecules, proteins). A method of analyzing a target ribonucleic acid (RNA), can include: (a) providing: (i) a target RNA, comprising a first target sequence and a second target sequence, and (ii) at least one probe including a first probe end hybridized to the first target sequence, and a second probe end hybridized to the second target sequence, wherein the first probe end hybridized to the first target sequence and the second probe end hybridized to the second target sequence are separated by a gap region. The method can further include filling the gap region and generating a probe-linked nucleic acid molecule including the at least one probe and the gap region.

Abstract: The present disclosure relates in some aspects to methods for analyzing target nucleic acids and their spatial locations in a biological sample. In some aspects, the presence/absence, amount, and/or identity of variant sequences (e.g., single nucleotide variations such as SNPs or point mutations) in a plurality of target nucleic acids in a cell or tissue sample are analyzed in situ in the sample. Also provided are compositions and kits for use in accordance with the methods.

Abstract: Provided herein are systems and methods for analyzing biomolecules (e.g., nucleic acid molecules, proteins). A method of nucleic acid analysis can comprise: (a) providing a sample comprising a cell comprising a target polynucleotide comprising a first exon segment and a second exon segment, wherein the first exon segment and the second exon segment flank opposite ends of a splice junction site of the target polynucleotide. The method can further comprise (b) contacting the cell with: (i) a first probe, wherein the first probe hybridizes to a first target sequence of the first exon segment, and (ii) a second probe, wherein the second probe hybridizes to a second target sequence of the second exon segment. The method can further comprise (c) linking the first probe and the second probe together, thereby generating a probe-linked nucleic acid molecule comprising the first probe and the second probe.

Abstract: The present disclosure relates generally to methods, compositions, and systems for processing nucleic acids from individual cells or cell populations. The present invention enables direct sequencing of full-length RNA molecules with no amplification steps. The present invention allows determination of RNA modifications in highly specific cell populations of any tissue.

Abstract: The present disclosure relates in some aspects to methods, systems, and kits for analyzing a biological sample comprising generating a rolling circle amplification product (RCP) using a target ribonucleic acid (RNA) as a primer. In some aspects, an RNA-cutting enzyme and a guide nucleic acid are used to generate a free 3? end of the target RNA to prime RCA.

Abstract: Compositions, kits and methods are described that comprise one or more constructs, each construct comprising a ligand attached or conjugated to a polymer construct, e.g., an oligonucleotide sequence, by a linker, each ligand binding specifically to a single target located in or on the surface of a cell. The polymer construct comprises a) an Amplification Handle; b) a Barcode that specifically identifies a single ligand; c) an optional Unique Molecular Identifier that is positioned adjacent to the Barcode on its 5? or 3? end; and d) an Anchor for hybridizing to a complementary sequence, e.g., for generation of a double-stranded oligonucleotide. These compositions are used in methods, including high throughput methods, for detecting one or more targets or epitopes in a biological sample. These compositions are also used in a high throughput method for characterizing a cell by simultaneous detection of one or more epitopes located in or on the cell and its transcriptome.

Abstract: Compositions, kits and methods are described that comprise one or more constructs, each construct comprising a ligand attached or conjugated to a polymer construct, e.g., an oligonucleotide sequence, by a linker, each ligand binding specifically to a single target located in or on the surface of a cell. The polymer construct comprises a) an Amplification Handle; b) a Barcode that specifically identifies a single ligand; c) an optional Unique Molecular Identifier that is positioned adjacent to the Barcode on its 5? or 3? end; and d) an Anchor for hybridizing to a complementary sequence, e.g., for generation of a double-stranded oligonucleotide. These compositions are used in methods, including high throughput methods, for detecting one or more targets or epitopes in a biological sample. These compositions are also used in a high throughput method for characterizing a cell by simultaneous detection of one or more epitopes located in or on the cell and its transcriptome.

Abstract: In some aspects, the present disclosure relates to methods, compositions and kits for analyzing a biological sample using a hybridization-based polymerization reaction (HPR). In some aspects, a target nucleic acid molecule is detected via an HPR such as hybridization chain reaction (HCR). In some aspects, the HPR is initiated and terminated by an initiator sequence and terminator sequence, respectively, and the initiator sequence and terminator sequence are associated with the same target nucleic acid molecule.

Abstract: Compositions, kits and methods are described that comprise one or more constructs, each construct comprising a ligand attached or conjugated to a polymer construct, e.g., an oligonucleotide sequence, by a linker, each ligand binding specifically to a single target located in or on the surface of a cell. The polymer construct comprises a) an Amplification Handle; b) a Barcode that specifically identifies a single ligand; c) an optional Unique Molecular Identifier that is positioned adjacent to the Barcode on its 5? or 3? end; and d) an Anchor for hybridizing to a complementary sequence, e.g., for generation of a double-stranded oligonucleotide. These compositions are used in methods, including high throughput methods, for detecting one or more targets or epitopes in a biological sample. These compositions are also used in a high throughput method for characterizing a cell by simultaneous detection of one or more epitopes located in or on the cell and its transcriptome.

Abstract: Compositions, kits and methods are described that comprise one or more constructs, each construct comprising a ligand attached or conjugated to a polymer construct, e.g., an oligonucleotide sequence, by a linker, each ligand binding specifically to a single target located in or on the surface of a cell. The polymer construct comprises a) an Amplification Handle; b) a Barcode that specifically identifies a single ligand; c) an optional Unique Molecular Identifier that is positioned adjacent to the Barcode on its 5? or 3? end; and d) an Anchor for hybridizing to a complementary sequence, e.g., for generation of a double-stranded oligonucleotide. These compositions are used in methods, including high throughput methods, for detecting one or more targets or epitopes in a biological sample. These compositions are also used in a high throughput method for characterizing a cell by simultaneous detection of one or more epitopes located in or on the cell and its transcriptome.