Abstract: Provided herein is a method for mapping rolling circle amplification (RCA) products that contain unique identifier sequences. The method generally involves (a) producing a complex comprising population of grid oligonucleotide molecules and a population of RCA products that each have a unique RCA product identifier sequence, wherein the grid oligonucleotides are hybridized directly or indirectly via a splint to complementary sites in the RCA products; (b) extending the grid oligonucleotide molecules that are hybridized to two RCA products to add the complements of the unique RCA product identifier sequences from the two RCA products to the grid oligonucleotide molecules; (c) sequencing the extended grid oligonucleotides; (d) analyzing the sequences to identify which pairs of unique RCA product identifier sequence complements have been added onto the grid oligonucleotides; and (e) making one or more physical maps of the immobilized RCA products using the pairs of sequences identified in (d).

Abstract: Provided herein is probe system comprising: a population of nucleic acid molecules that have an extendible end, a first set of barcoded particles that each have a nucleotide sequence comprising: (i) a binding sequence that is complementary to the extendible end of the nucleic acid molecules, (ii) a unique particle identifier sequence, and (iii) a first template sequence, and a second set of barcoded particles that each have a nucleotide sequence comprising: (i) the first template sequence and (ii) a unique particle identifier sequence. In use, extension of the nucleic acid molecules using the first set of barcoded particles of as a template produces extensions products that contain the complement of a unique particle identifier sequence of a particle and the complement of the first template sequence. Methods of using the probe system to map binding events in or on a cellular sample are also provided.

Abstract: Provided herein is a method comprising producing rolling circle amplification (RCA) products that are immobilized in or on cells, wherein each RCA product has an RCA product identifier sequence that distinguishes the RCA product from other RCA products that are immobilized in or on the cells; while the RCA products are immobilized in or on cells, producing nucleic acid products that contain RCA product identifier sequences or complements thereof from adjacent RCA products; for each of a plurality of the nucleic acid products, identifying which RCA product identifier sequences or complements thereof are in the nucleic acid product; and making a physical map of at least some of the RCA products using the identified RCA product identifier sequences or complements thereof.

Abstract: Provided herein is a method comprising producing rolling circle amplification (RCA) products that are immobilized in or on cells, wherein each RCA product has an RCA product identifier sequence that distinguishes the RCA product from other RCA products that are immobilized in or on the cells; while the RCA products are immobilized in or on cells, producing nucleic acid products that contain RCA product identifier sequences or complements thereof from adjacent RCA products; for each of a plurality of the nucleic acid products, identifying which RCA product identifier sequences or complements thereof are in the nucleic acid product; and making a physical map of at least some of the RCA products using the identified RCA product identifier sequences or complements thereof.

Abstract: A method for labeling a biological sample is provided. In some embodiments, the method may comprise: labeling the biological sample with a one or more primary antibody-oligonucleotide conjugates to produce a labeled sample, incubating the labeled sample with a secondary antibody that recognizes the primary antibody of the primary antibody-oligonucleotide conjugates, thereby cross-linking the primary antibody and producing a cross-linked sample, performing one or more molecular reactions on the oligonucleotide of the primary antibody-oligonucleotide conjugates to produce a nucleic acid product; and detecting the nucleic acid product. Kits for practicing the method are also provided.

Abstract: Described herein is a complex comprising multiple nucleic acid molecules that are hybridized together, each comprising, from 5? to 3?, a first complementary sequence, a spacer sequence and a second complementary sequence, and either/or a 5? end sequence that is 5? of the first complementary sequence and terminates in a 5? phosphate and a 3? end sequence that is 3? of the second complementary sequence and terminates in a 3? hydroxyl. In this complex: the first complementary sequence of one molecule is directly or indirectly hybridized with the second complementary sequence of another molecule in the complex and the spacer sequence and the 3? and/or 5? end sequences are single-stranded. Methods of making and using the complex are also provided.

Abstract: Described herein is a complex comprising multiple nucleic acid molecules that are hybridized together, each comprising, from 5? to 3?, a first complementary sequence, a spacer sequence and a second complementary sequence, and either/or a 5? end sequence that is 5? of the first complementary sequence and terminates in a 5? phosphate and a 3? end sequence that is 3? of the second complementary sequence and terminates in a 3? hydroxyl. In this complex: the first complementary sequence of one molecule is directly or indirectly hybridized with the second complementary sequence of another molecule in the complex and the spacer sequence and the 3? and/or 5? end sequences are single-stranded. Methods of making and using the complex are also provided.

Abstract: Provided herein is a method for mapping rolling circle amplification (RCA) products that contain unique identifier sequences. The method generally involves (a) producing a complex comprising population of grid oligonucleotide molecules and a population of RCA products that each have a unique RCA product identifier sequence, wherein the grid oligonucleotides are hybridized directly or indirectly via a splint to complementary sites in the RCA products; (b) extending the grid oligonucleotide molecules that are hybridized to two RCA products to add the complements of the unique RCA product identifier sequences from the two RCA products to the grid oligonucleotide molecules; (c) sequencing the extended grid oligonucleotides; (d) analyzing the sequences to identify which pairs of unique RCA product identifier sequence complements have been added onto the grid oligonucleotides; and (e) making one or more physical maps of the immobilized RCA products using the pairs of sequences identified in (d).

Abstract: Provided herein is probe system comprising: a population of nucleic acid molecules that have an extendible end, a first set of barcoded particles that each have a nucleotide sequence comprising: (i) a binding sequence that is complementary to the extendible end of the nucleic acid molecules, (ii) a unique particle identifier sequence, and (iii) a first template sequence, and a second set of barcoded particles that each have a nucleotide sequence comprising: (i) the first template sequence and (ii) a unique particle identifier sequence. In use, extension of the nucleic acid molecules using the first set of barcoded particles of as a template produces extensions products that contain the complement of a unique particle identifier sequence of a particle and the complement of the first template sequence. Methods of using the probe system to map binding events in or on a cellular sample are also provided.

Abstract: Provided herein is probe system comprising: a population of nucleic acid molecules that have an extendible end, a first set of barcoded particles that each have a nucleotide sequence comprising: (i) a binding sequence that is complementary to the extendible end of the nucleic acid molecules, (ii) a unique particle identifier sequence, and (iii) a first template sequence, and a second set of barcoded particles that each have a nucleotide sequence comprising: (i) the first template sequence and (ii) a unique particle identifier sequence. In use, extension of the nucleic acid molecules using the first set of barcoded particles of as a template produces extensions products that contain the complement of a unique particle identifier sequence of a particle and the complement of the first template sequence. Methods of using the probe system to map binding events in or on a cellular sample are also provided.

Abstract: Provided herein is a method for making a physical map of a population of barcoded particles. In some embodiments, the method may involve: producing a complex comprising: i. a population of barcoded particles, wherein the barcoded particles are uniquely barcoded by surface-tethered oligonucleotides that have unique particle identifier sequences; and ii. a population of bridging moieties that comprises oligonucleotide sequences; wherein the bridging moieties are hybridized directly or indirectly to complementary sites in the surface-tethered oligonucleotides; performing a ligation, polymerization and/or a gap-fill/ligation reaction on the complex, thereby producing reaction products that comprise pairs of unique particle identifier sequences or complements thereof from adjacent barcoded particles: sequencing the reaction products, analyzing the sequences to making one or more physical maps of the barcoded particles. Systems for practicing the method are also provided.

Abstract: Described herein is a complex comprising multiple nucleic acid molecules that are hybridized together, each comprising, from 5? to 3?, a first complementary sequence, a spacer sequence and a second complementary sequence, and either/or a 5? end sequence that is 5? of the first complementary sequence and terminates in a 5? phosphate and a 3? end sequence that is 3? of the second complementary sequence and terminates in a 3? hydroxyl. In this complex: the first complementary sequence of one molecule is directly or indirectly hybridized with the second complementary sequence of another molecule in the complex and the spacer sequence and the 3? and/or 5? end sequences are single-stranded. Methods of making and using the complex are also provided.

Abstract: Provided herein is probe system comprising: a population of nucleic acid molecules that have an extendible end. a first set of barcoded particles that each have a nucleotide sequence comprising: (i) a binding sequence that is complementary to the extendible end of the nucleic acid molecules. (ii) a unique particle identifier sequence. and (iii) a first template sequence. and a second set of barcoded particles that each have a nucleotide sequence comprising: (i) the first template sequence and (ii) a unique particle identifier sequence. In use. extension of the nucleic acid molecules using the first set of barcoded particles of as a template produces extensions products that contain the complement of a unique particle identifier sequence of a particle and the complement of the first template sequence. Methods of using the probe system to map binding events in or on a cellular sample are also provided.

Abstract: Provided herein is a method for mapping rolling circle amplification (RCA) products that contain unique identifier sequences. The method generally involves (a) producing a complex comprising population of grid oligonucleotide molecules and a population of RCA products that each have a unique RCA product identifier sequence, wherein the grid oligonucleotides are hybridized directly or indirectly via a splint to complementary sites in the RCA products; (b) extending the grid oligonucleotide molecules that are hybridized to two RCA products to add the complements of the unique RCA product identifier sequences from the two RCA products to the grid oligonucleotide molecules; (c) sequencing the extended grid oligonucleotides; (d) analyzing the sequences to identify which pairs of unique RCA product identifier sequence complements have been added onto the grid oligonucleotides; and (e) making one or more physical maps of the immobilized RCA products using the pairs of sequences identified in (d).

Abstract: The present invention relates to a proximity probe based detection assay (“proximity assay”) for an analyte in a sample, specifically a proximity probe extension assay (PEA), an in particular to an improvement in the method to reduce non-specific “background” signals, wherein the improvement comprises the use in such assays of a component comprising 3? exonuclease activity, said method comprising: (a) contacting said sample with at least one set of at least first and second proximity probes, which probes each comprise an analyte-binding domain and a nucleic acid domain and can simultaneously bind to the analyte; (b) allowing the nucleic acid domains of the proximity probes to interact with each other upon binding of said proximity probes to said analyte, wherein said interaction comprises the formation of a duplex; (c) contacting said sample with a component comprising 3? exonuclease activity; (d) extending the 3? end of at least one nucleic acid domain of said duplex to generate an extension product, wherein

Abstract: The present invention relates to a proximity probe based detection assay (“proximity assay”) for an analyte in a sample, specifically a proximity probe extension assay (PEA), an in particular to an improvement in the method to reduce non-specific “background” signals, wherein the improvement comprises the use in such assays of a component comprising 3? exonuclease activity, said method comprising: (a) contacting said sample with at least one set of at least first and second proximity probes, which probes each comprise an analyte-binding domain and a nucleic acid domain and can simultaneously bind to the analyte; (b) allowing the nucleic acid domains of the proximity probes to interact with each other upon binding of said proximity probes to said analyte, wherein said interaction comprises the formation of a duplex; (c) contacting said sample with a component comprising 3? exonuclease activity; (d) extending the 3? end of at least one nucleic acid domain of said duplex to generate an extension product, wherein

Abstract: The present invention relates to a proximity probe based detection assay (“proximity assay”) for an analyte in a sample, specifically a proximity probe extension assay (PEA), an in particular to an improvement in the method to reduce non-specific “background” signals, wherein the improvement comprises the use in such assays of a hyperthermophilic polymerase, said method comprising: (a) contacting said sample with at least one set of at least first and second proximity probes, which probes each comprise an analyte-binding domain and a nucleic acid domain and can simultaneously bind to the analyte; (b) allowing the nucleic acid domains of the proximity probes to interact with each other upon binding of said proximity probes to said analyte, wherein said interaction comprises the formation of a duplex; (c) extending the 3? end of at least one nucleic acid domain of said duplex to generate an extension product, wherein the extension reaction comprises increasing the temperature of assay above room temperature and