Methods for identifying co-occurrence of nucleic acid segments in a nucleic acid sample from a specimen including obtaining a nucleic acid sample from a specimen, determining sequences of first and second nucleic acid segments in nucleic acid fragments of the sample to generate a first and second sets of sequences, generating a first and second sets of probes from the first and second sets of sequences, exposing a detection sample to a member of the first set of probes and a member of the second set of probes, performing a hybridization analysis to determine whether the members of the first and second sets of probes hybridize to the detection sample, and determining whether the first and second nucleic acid segments co-occur in a common cell of the specimen.

Methods for identifying co-occurrence of nucleic acid segments in a nucleic acid sample from a specimen including obtaining a nucleic acid sample from a specimen, determining sequences of first and second nucleic acid segments in nucleic acid fragments of the sample to generate a first and second sets of sequences, generating a first and second sets of probes from the first and second sets of sequences, exposing a detection sample to a member of the first set of probes and a member of the second set of probes, performing a hybridization analysis to determine whether the members of the first and second sets of probes hybridize to the detection sample, and determining whether the first and second nucleic acid segments co-occur in a common cell of the specimen.

The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.

The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.

The present invention relates to a multiplicity of nucleic acid probes, a composition comprising said probes and uses thereof. The invention relates to a multiplicity of non-beacon, hairpin loop forming nucleic acid probes. In particular, the invention relates to a multiplicity of nucleic acid probes, each nucleic acid probe comprising a nucleic acid sequence complementary to the target nucleic acid sequence; wherein said nucleic acid probes are capable of forming a multimer in-situ with at least a neighbouring probe. The invention relates to the use of nucleic acid probes to detect the presence or absence of organisms in biological samples.

The present invention relates to a multiplicity of nucleic acid probes, a composition comprising said probes and uses thereof. The invention relates to a multiplicity of non-beacon, hairpin loop forming nucleic acid probes. In particular, the invention relates to a multiplicity of nucleic acid probes, each nucleic acid probe comprising a nucleic acid sequence complementary to the target nucleic acid sequence; wherein said nucleic acid probes are capable of forming a multimer in-situ with at least a neighbouring probe. The invention relates to the use of nucleic acid probes to detect the presence or absence of organisms in biological samples.

A method of detecting target nucleic acids, including small non-coding RNAs (sncRNAs), microRNAs (miRNAs), small interfering RNAs (siRNAs), PIWI-interacting RNA (piRNA), or antisense oligonucleotides (ASO) molecules, in a cell, comprising a post-fixation step using an aldehyde-containing fixative after the initial fixation step prior to in situ hybridization.

A method of detecting target nucleic acids, including small non-coding RNAs (sncRNAs), microRNAs (miRNAs), small interfering RNAs (siRNAs), PIWI-interacting RNA (piRNA), or antisense oligonucleotides (ASO) molecules, in a cell, comprising a post-fixation step using an aldehyde-containing fixative after the initial fixation step prior to in situ hybridization.

Provided herein are methods for spatial analysis using targeted RNA depletion.

Provided herein are methods for spatial analysis using targeted RNA depletion.