Provided herein are methods of determining a surgical margin and the site and size of a tissue to be resected from a subject, and methods of use thereof.

Disclosed herein, inter alia, are substrates, kits, and efficient methods of preparing and sequencing two or more regions of a double-stranded polynucleotide.

Disclosed herein, inter alia, are substrates, kits, and efficient methods of preparing and sequencing two or more regions of a double-stranded polynucleotide.

Disclosed herein are compositions and methods for determining a presence or abundance of an analyte in a biological sample. The methods disclosed herein include: (a) providing a biological sample on a substrate comprising a plurality of capture probes, wherein a capture probe of the plurality of capture probes comprises a capture domain; (b) releasing the analyte from the biological sample; (c) affixing a stretching moiety to the analyte; (d) hybridizing the analyte to the capture domain of the capture probe; (e) applying a stretching force to the stretching moiety, thereby elongating the analyte hybridized to the capture domain; and (f) generating an extended capture probe using the analyte as a template.

Disclosed herein are compositions and methods for determining a presence or abundance of an analyte in a biological sample. The methods disclosed herein include: (a) providing a biological sample on a substrate comprising a plurality of capture probes, wherein a capture probe of the plurality of capture probes comprises a capture domain; (b) releasing the analyte from the biological sample; (c) affixing a stretching moiety to the analyte; (d) hybridizing the analyte to the capture domain of the capture probe; (e) applying a stretching force to the stretching moiety, thereby elongating the analyte hybridized to the capture domain; and (f) generating an extended capture probe using the analyte as a template.

The present application provides methods, compositions, and kits for analyzing a biological sample embedded in a three-dimensional polymerized matrix using a primer-exchange reaction (PER). In some embodiments, the methods comprise contacting the sample with a nucleic acid molecule that directly or indirectly binds to an analyte in the sample and immobilizing the nucleic acid molecule in the matrix, wherein the nucleic acid molecule comprises a free 3′ priming region for initiation of PER. In some embodiments, the methods enable sensitive detection of the identity and relative position of analytes in the sample.

The present application provides methods, compositions, and kits for analyzing a biological sample embedded in a three-dimensional polymerized matrix using a primer-exchange reaction (PER). In some embodiments, the methods comprise contacting the sample with a nucleic acid molecule that directly or indirectly binds to an analyte in the sample and immobilizing the nucleic acid molecule in the matrix, wherein the nucleic acid molecule comprises a free 3′ priming region for initiation of PER. In some embodiments, the methods enable sensitive detection of the identity and relative position of analytes in the sample.

Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample.

Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample.

The present disclosure provides methods and systems for performing single-molecule detection using fabricated integrated on-chip devices. In an aspect, the present disclosure provides a method for on-chip detection of an array of biological, chemical, or physical entities, comprising: (a) providing an array of light sensing devices; (b) immobilizing the array of biological, chemical, or physical entities on a substrate of the array of light sensing devices; (c) exposing the array of biological, chemical, or physical entities to electromagnetic radiation sufficient to excite the array of biological, chemical, or physical entities, thereby producing an emission signal of the array of biological, chemical, or physical entities; (d) using the array of light sensing devices, acquiring pixel information of the emission signal of the array of biological, chemical, or physical entities without scanning the array of light sensing devices across the array of biological, chemical, or physical entities; and (d) detecting the array of biological, chemical, or physical entities based at least in part on the acquired pixel information.