Abstract: Methods of producing partitioned single cell/barcoded bead compositions are provided. Aspects of the methods include: contacting a composition of encapsulated single cells, e.g. double emulsion single cell droplets or gel encapsulated single cells, with a plurality of microwells such that at least a portion of the plurality of microwells include a sole deposited encapsulated cell, e.g., a sole deposited cell containing double emulsion droplet or gel bead; releasing the single cells from their encapsulation, e.g., by disrupting deposited double emulsion single cell droplets or dissolving gel beads, to generate microwells comprising released single cells; and introducing barcoded beads into microwells comprising released single cells to produce partitioned single cell/barcoded bead compositions. Also provided are compositions for practicing methods of the invention. The methods and compositions of the invention find use in a variety of applications, such as single cell sequencing applications.

Abstract: Methods of producing a plurality of distinguishably fluorescently barcoded particle, e.g., cellular, bead, etc., samples, e.g., for use in the multiplex flow cytometric workflows, are provided. Aspects of the methods include: providing a plurality of particle, e.g., cellular, bead, etc., samples; and labeling different particle, e.g., cellular, bead, etc., samples of the plurality with unique fluorescent barcodes, wherein a given fluorescent barcode comprises one or more fluorescently labeled specific binding members that specifically bind to a particle marker. Also provided are compositions for practicing methods of the invention.

Abstract: Some embodiments disclosed herein provide a plurality of compositions each comprising a protein binding reagent conjugated with an oligonucleotide. The oligonucleotide comprises a unique identifier for the protein binding reagent it is conjugated with, and the protein binding reagent is capable of specifically binding to a protein target. Further disclosed are methods and kits for quantitative analysis of a plurality of protein targets in a sample and for simultaneous quantitative analysis of protein and nucleic acid targets in a sample. Also disclosed herein are systems and methods for preparing a labeled biomolecule reagent, including a labeled biomolecule agent comprising a protein binding reagent conjugated with an oligonucleotide.

Abstract: Some embodiments disclosed herein provide a plurality of compositions each comprising a protein binding reagent conjugated with an oligonucleotide. The oligonucleotide comprises a unique identifier for the protein binding reagent it is conjugated with, and the protein binding reagent is capable of specifically binding to a protein target. Further disclosed are methods and kits for quantitative analysis of a plurality of protein targets in a sample and for simultaneous quantitative analysis of protein and nucleic acid targets in a sample. Also disclosed herein are systems and methods for preparing a labeled biomolecule reagent, including a labeled biomolecule agent comprising a protein binding reagent conjugated with an oligonucleotide.

Abstract: 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.

Abstract: Aspects of the present disclosure include systems for use in preparing an epitope tagged biomolecule reagent. A reagent preparatory apparatus for preparing the epitope tagged biomolecule reagent from an activated biomolecule and activated epitope tag is also described. Methods for communicating and receiving an epitope tagged biomolecule reagent request and preparing the subject epitope tagged biomolecule reagents are also provided.

Abstract: Disclosed herein include methods, compositions, and kits suitable for spectral unmixing and compensation in multi-parameter flow cytometry. Disclosed herein include reagents which comprise two antibodies conjugated to one another to form a bispecific reagent (e.g., a bispecific probe). A first antibody can have affinity for a highly expressed antigen on the surface of a cell of interest and a second antibody can have affinity for each of the antibody-dye conjugates in a multi-parameter panel. There are provided, in some embodiments, methods of using the bispecific reagent to determine spillover, perform compensation, and generate a compensation matrix.

Abstract: Fluorogenic sensors for a target analyte are provided. The fluorogenic sensors can include a water soluble light harvesting multichromophore and a fluorogenic dye covalently linked to the multichromophore and in energy-receiving proximity therewith. Aspects of the fluorogenic sensors include selective recognition of the target analyte by chemical reaction or by specific binding. In some cases, the linked fluorogenic dye includes a lactone or spiro-lactone group that is configured to chemically react with a target analyte via lactone ring-opening to produce a fluorescent dye configured for excitation by the multichromophore. Also provided are labelled specific binding members that include the subject dyes. Methods of evaluating a sample for the presence of a target analyte and methods of labelling a target molecule in which the subject fluorogenic sensors find use are provided. Systems, devices and kits for practicing the subject methods are provided.

Abstract: Disclosed herein include systems, methods, compositions, and kits for performing intracellular AbSeq assays. There are provided, in some embodiments, methods for measuring intracellular target expression. The method can comprise fixing and permeabilizing a plurality of cells before contacting with a plurality of intracellular target-binding reagents capable of specifically binding to an intracellular target. Intracellular target-binding reagents can comprise an intracellular target-binding reagent specific oligonucleotide comprising a unique intracellular target identifier for the intracellular target-binding reagent specific oligonucleotide. The method can further comprise removing the permeabilizing agent and reversing the fixation.

Abstract: 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 bispecific probes comprising an anchor probe capable of specifically binding to a surface cellular target of a cell, and a capture probe capable of specifically binding to a secreted factor secreted by a cell that is associated with the capture probe. Also disclosed herein include secreted factor-binding reagents capable of specifically binding to a secreted factor bound by a capture probe, where 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.

Abstract: Disclosed herein include systems, methods, compositions, and kits for sample identification. A sample indexing composition can comprise, for example, a protein binding reagent associated with a sample indexing oligonucleotide. Different sample indexing compositions can include sample indexing oligonucleotides with different sequences. Sample origin of cells can be identified based on the sequences of the sample indexing oligonucleotides. Sample indexing oligonucleotides can be barcoded using barcoded and lengthened using daisy-chaining primers.

Abstract: Disclosed herein include systems, methods, compositions, and kits for sample identification. A sample indexing composition can comprise, for example, a protein binding reagent associated with a sample indexing oligonucleotide. Different sample indexing compositions can include sample indexing oligonucleotides with different sequences. Sample origin of cells can be identified based on the sequences of the sample indexing oligonucleotides. Sample indexing oligonucleotides can be barcoded using barcoded and lengthened using daisy-chaining primers.

Abstract: Photostable polymeric tandem dyes are provided. The photostable polymeric tandem dyes include a water soluble light harvesting multichromophore and a luminescent metal complex covalently linked to the multichromophore and in energy-receiving proximity therewith. Also provided are labelled specific binding members that include the subject dyes. Methods of evaluating a sample for the presence of a target analyte and methods of labelling a target molecule in which the subject polymeric tandem dyes find use are also provided. Systems and kits for practicing the subject methods are also provided.

Abstract: Fluorogenic sensors for a target analyte are provided. The fluorogenic sensors can include a water soluble light harvesting multichromophore and a fluorogenic dye covalently linked to the multichromophore and in energy-receiving proximity therewith. Aspects of the fluorogenic sensors include selective recognition of the target analyte by chemical reaction or by specific binding. In some cases, the linked fluorogenic dye includes a lactone or spiro-lactone group that is configured to chemically react with a target analyte via lactone ring-opening to produce a fluorescent dye configured for excitation by the multichromophore. Also provided are labelled specific binding members that include the subject dyes. Methods of evaluating a sample for the presence of a target analyte and methods of labelling a target molecule in which the subject fluorogenic sensors find use are provided. Systems, devices and kits for practicing the subject methods are provided.

Abstract: Disclosed herein include systems, methods, compositions, and kits for sample identification. A sample indexing composition can comprise, for example, a protein binding reagent associated with a sample indexing oligonucleotide. Different sample indexing compositions can include sample indexing oligonucleotides with different sequences. Sample origin of cells can be identified based on the sequences of the sample indexing oligonucleotides. Sample indexing oligonucleotides can be barcoded using barcoded and lengthened using daisy-chaining primers.

Abstract: Methods are provided for distinguishing a cardiomyocyte subset in a heterogeneous cellular sample. Aspects of the methods include contacting the heterogeneous cellular sample with a cell surface marker specific binding member, and then distinguishing a cardiomyocyte subset of the cellular sample based on binding to the cell surface marker specific binding member. Also provided are devices, compositions and kits that find use in performing the subject methods.

Abstract: Aspects of the present disclosure include systems for use in preparing an epitope tagged biomolecule reagent. A reagent preparatory apparatus for preparing the epitope tagged biomolecule reagent from an activated biomolecule and activated epitope tag is also described. Methods for communicating and receiving an epitope tagged biomolecule reagent request and preparing the subject epitope tagged biomolecule reagents are also provided.

Abstract: Some embodiments disclosed herein provide a plurality of compositions each comprising a protein binding reagent conjugated with an oligonucleotide. The oligonucleotide comprises a unique identifier for the protein binding reagent it is conjugated with, and the protein binding reagent is capable of specifically binding to a protein target. Further disclosed are methods and kits for quantitative analysis of a plurality of protein targets in a sample and for simultaneous quantitative analysis of protein and nucleic acid targets in a sample. Also disclosed herein are systems and methods for preparing a labeled biomolecule reagent, including a labeled biomolecule agent comprising a protein binding reagent conjugated with an oligonucleotide.

Abstract: Proteinaceous specific binding members that specifically bind to a polymeric dye are provided. Also provided are methods of using the specific binding members, e.g., in separating a polymeric dye-labeled cell from a sample, in analyte detection, etc., as described herein. Kits and systems for practicing the subject methods are also provided.

Abstract: Photostable polymeric tandem dyes are provided. The photostable polymeric tandem dyes include a water soluble light harvesting multichromophore and a luminescent metal complex covalently linked to the multichromophore and in energy-receiving proximity therewith. Also provided are labelled specific binding members that include the subject dyes. Methods of evaluating a sample for the presence of a target analyte and methods of labelling a target molecule in which the subject polymeric tandem dyes find use are also provided. Systems and kits for practicing the subject methods are also provided.