Systems, methods, compositions, and kits for measuring secreted factors from cells are disclosed herein, including those capable of determining single cell secretion activity and protein expression and/or gene expression simultaneously. Disclosed herein include solid supports comprising a plurality of capture probes capable of specifically binding to at least one of the plurality of secreted factors secreted by a single cell. Also disclosed herein include secreted factor-binding reagents capable of specifically binding to a secreted factor bound by a capture probe. A secreted factor-binding reagent can comprise a secreted factor-binding reagent specific oligonucleotide comprising a unique factor identifier sequence for the secreted factor-binding reagent.

Aspects of the disclosure provide methods of determining molecular barcode content based on binding interactions between a barcode recognition molecule and a molecular barcode. In some aspects, the disclosure relates to methods comprising contacting a molecular barcode with a barcode recognition molecule that binds to one or more sites on the molecular barcode, detecting a series of signal pulses, and determining the barcode content based on a barcode-specific pattern in the series of signal pulses.

Disclosed herein include systems, methods, compositions, and kits for measuring the secretion level of a secreted factor of a single cell. Disclosed herein include solid supports comprising a plurality of capture probes capable of specifically binding to secreted factors secreted by a single cell. In some of the embodiments, at least two of the capture probes are capable of binding different secreted factors. Also disclosed herein include secreted factor-binding reagents capable of specifically binding to a secreted factor bound by a capture probe. Secreted factor-binding reagents can comprise a detectable moiety, or a precursor thereof. Secreted factor-binding reagents capable of binding the same secreted factor comprise the same detectable moiety, or a precursor thereof, and secreted factor-binding reagents capable of binding different secreted factors can comprise different detectable moieties, or precursors thereof.

Provided for herein is a polynucleotide-modified bioconjugate comprising a substrate such as an antibody or bead linked to a conjugate component via a nucleic acid linker. Also provided are methods of making and using such bioconjugates. Conjugation methods for creating the bioconjugate are stable, not chemically harsh, and efficient enough that post-conjugation purification may not be required. Further this disclosure provides for reducing the logistic overheads related to product lines by eliminating the need for many unique linkers per conjugation pair.

Methods for imaging are described, including, but not limited to a method comprising: (1) contacting a sample being tested for the presence of one or more targets with one or more target-specific binding partners, wherein each target-specific binding partner is linked to a docking strand, and wherein target-specific binding partners of different specificity are linked to different docking strands, (2) optionally removing unbound target-specific binding partners, (3) contacting the sample with antigen-bound imager strands and antigen-specific binding partners linked (directly or indirectly) to optical labels, wherein the antigen-bound imager strands have complementarity to a docking strand, directly or indirectly, and wherein each antigen-specific binding partner is linked to one or more optical labels, and wherein antigen-specific binding partners of different specificity are linked to distinct optical labels, (4) optionally removing unbound antigen-bound imager strands and/or antigen-specific binding partners, (5) imaging the sample to detect bound labeled antigen-specific binding partners, (6) optionally removing/extinguishing signal from the optical labels, and (7) optionally repeating steps (1)-(6), or any subset thereof.

Disclosed herein include systems, methods, compositions, and kits suitable for the use of dextramers in single cell analysis. In some embodiments, one or more primers allowing generation of separate libraries for proteins (e.g., antibodies) and for dextramers are used.

A cellular coding construct uniquely codes a cellular entity and includes a laser particle and a structurally coded oligonucleotide. The structurally coded oligonucleotide and the laser particle have a physical association with each other and are configured for physical association with the cellular entity and also configured for distinctive identification of the cellular entity.

Methods and compositions for multiplexed protein-protein interaction profiling (e.g., immunoprofiling), based on nucleic acid tagging of polypeptides (e.g., by RNA display) are described. In some embodiments the described compositions and methods utilize a library of prey polypeptide targets linked to prey RNAs encoding them, and a population of bait polypeptides, e.g., a mixture of antibodies, that bind to one or more of the prey polypeptide targets and are used to isolate and identify the bound prey polypeptide targets by amplification of their associated prey RNAs and sequencing of the corresponding cDNAs. In other embodiments the prey polypeptide targets are linked to DNA Bar Codes, which serve as unique identifiers of the tagged polypeptide.

Provided herein, in some embodiments, are systems, methods, compositions, and kits for detecting and quantifying analytes using a primary analyte binding molecule conjugated to a nucleic acid template.

Some embodiments of the systems and methods provided herein relate to an assay. Some such embodiments include multiplex affinity probes and an antigen probe. multiplex affinity probes and an antigen probe Some embodiments include contacting a biological sample with the probes, wherein target binding agents such as antibodies in the biological sample compete away the multiplex affinity probes from binding to the antigen probe. Some such embodiments include detecting a decrease in binding of the multiplex affinity probes to the antigen probe, thereby indicating the presence or an amount of the target binding agents in the biological sample.