The present invention relates to a method for preparing probes for target nucleic acids targets. This method includes: a) obtaining a target DNA sequence of interest; b) adding adapter sequences to both ends of a fragmented DNA sequence while fragmenting the target DNA sequence by using transposase; and c) obtaining the fragmented DNA sequence by using the adapter sequences to generate the probes. The method provided by the present invention can efficiently, easily, and accurately mark the position of the genome at the level of one kilobase resolution.

The present invention relates to a method for preparing probes for target nucleic acids targets. This method includes: a) obtaining a target DNA sequence of interest; b) adding adapter sequences to both ends of a fragmented DNA sequence while fragmenting the target DNA sequence by using transposase; and c) obtaining the fragmented DNA sequence by using the adapter sequences to generate the probes. The method provided by the present invention can efficiently, easily, and accurately mark the position of the genome at the level of one kilobase resolution.

The present disclosure in some aspects relates to methods and compositions for accurately detecting and quantifying analytes present at high levels, such as highly expressed genes in a sample. In some embodiments, a probe-resolution barcode sequence disclosed herein does not specifically correspond to any particular target analyte(s) but can be used to resolve dense optical signals due to spatially overlapping signals associated with different molecules of a target analyte, thereby enabling resolution of signals in a dense “spot” and accurate counting of spots associated with molecules that are in spatial proximity. Also provided are kits comprising probes for use in such methods.

The present disclosure in some aspects relates to methods and compositions for accurately detecting and quantifying analytes present at high levels, such as highly expressed genes in a sample. In some embodiments, a probe-resolution barcode sequence disclosed herein does not specifically correspond to any particular target analyte(s) but can be used to resolve dense optical signals due to spatially overlapping signals associated with different molecules of a target analyte, thereby enabling resolution of signals in a dense “spot” and accurate counting of spots associated with molecules that are in spatial proximity. Also provided are kits comprising probes for use in such methods.

The present disclosure in some aspects relates to methods and compositions for accurately detecting and quantifying multiple analytes present in a biological sample. In some aspects, the methods and compositions provided herein address one or more issues associated with the stability and/or size of nucleic acid structures, such as RCPs, in the biological sample without the use of exogenously added oligonucleotide compaction probes. In some embodiments, provided herein are methods involving the use of self-hybridizing hybridizing regions for compacting and/or stabilizing nucleic acid concatemers (e.g., RCPs). In some embodiments, dynamic inter-strand annealing between tandem units of an RCP is used for compaction and/or stabilization. In some embodiments, short palindromic regions in an RCP are used for compaction and/or stabilization.

The present disclosure in some aspects relates to methods and compositions for accurately detecting and quantifying multiple analytes present in a biological sample. In some aspects, the methods and compositions provided herein address one or more issues associated with the stability and/or size of nucleic acid structures, such as RCPs, in the biological sample without the use of exogenously added oligonucleotide compaction probes. In some embodiments, provided herein are methods involving the use of self-hybridizing hybridizing regions for compacting and/or stabilizing nucleic acid concatemers (e.g., RCPs). In some embodiments, dynamic inter-strand annealing between tandem units of an RCP is used for compaction and/or stabilization. In some embodiments, short palindromic regions in an RCP are used for compaction and/or stabilization.

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

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

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.