Abstract: The present disclosure relates in some aspects to methods and compositions for in situ detection of an analyte in a biological sample embedded in a matrix that is attached to metal nanoparticles. In some embodiments, the detection involves generation of a fluorescent signal that is enhanced by the metal nanoparticles. The fluorescent signal can be detected at a 3-dimensional (3D) location in the matrix which corresponds to the 3D location of the analyte in the biological sample.

Abstract: The present disclosure relates in some aspects to methods and compositions for assessing system performance for in situ analyte detection. In some aspects, performance of an individual instrument can be assessed, or the performance of two or more instruments can be assessed and optionally compared. In some aspects, disclosed herein is a method comprising using rolling circle amplification products (RCPs) deposited on a cell-free and tissue-free quality control (QC) slide to assess performance of instrument workflow, where an instrument is used to decode signals associated with the RCPs on the QC slide. Quality metrics associated with the decoding (e.g., a percentage of RCPs successfully decoded to genes) can be used to qualify a system comprising the instrument and reagents for in situ analyte detection in cells or tissue samples, e.g., using in situ probe hybridization or in situ sequencing performed on the instrument.

Abstract: Provided herein are methods of releasing an extended capture probe from a substrate and uses of the same.