Abstract: The present disclosure relates generally to the field of immunology, and particularly relates to compositions, methods, and systems for the analysis and generation of antigen-binding molecules produced by immune cells obtained from tissue samples (e.g., antibodies produced by B cells in tumor tissue samples or TCRs produced by T cells in tumor tissue samples) using spatial methodologies, and for the production and characterization of recombinant antigen-binding molecules (e.g., antibodies, TCRs) with desired properties.

Abstract: In some embodiments, provided herein is an integrated assay of a biological sample comprising an in situ assay module and a spatial assay module. The in situ assay comprises analyzing binding between nucleic acid probes and a first analyte at a spatial location of the biological sample. In some embodiments, the method further comprises providing conditions to allow spatially barcoded capture agents to capture a second analyte for analysis in the spatial assay module.

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.