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:
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:
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:
Scaffolded chromophores for nucleic acid detection and systems, methods, and uses thereof are provided. Certain embodiments are directed to nucleic acid probes that include a nucleic acid that is complementary to a target sequence. The probe further includes a dye structure linked to a first end of the nucleic acid and includes a non-conjugated polymeric backbone with one or more donor fluorophores linked to the polymeric backbone and one or more acceptor fluorophores linked to the polymeric backbone, where the donor and acceptor fluorophores are in energy transfer relationship. Such probes can further include a quencher attached to a second end of the nucleic acid, where the quencher and one or more acceptor fluorophores are in an energy transfer relationship. Additional embodiments include a second nucleic acid probe including a second nucleic acid that is complementary to a different target sequence.
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:
Disclosed herein include systems, methods, compositions, and kits for determining the spatial location and copy number of targets (e.g., nucleic acid targets, cellular component targets) in a sample. There are provided, in some embodiments, substrates comprising a plurality of spatial regions. A plurality of oligonucleotide barcodes can be associated with each of the spatial regions and can comprise a predetermined spatial label. Oligonucleotide barcodes of the same spatial region can comprise the same spatial label, and oligonucleotide barcodes of the different spatial regions can comprise different spatial labels. The method can comprise contacting the substrate with a sample such that each distinct spatial region contacts a distinct spatial location of the sample. The method can comprise in situ extension (e.g., reverse transcription) of the oligonucleotide barcodes.
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:
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 fmd use in performing the subject methods.
Abstract:
The inventors disclose methods and systems that provide for the isolation and purification of neurons directly from heterogeneous cell cultures. The expression of various cell adhesion molecules was examined in pluripotent stem cells. Changes in the expression of one or more of these molecules correlates with the progression of cells from non-lineage committed to neural cells. Using one or more antibodies for these molecules in combination with antibodies specific for CD200 will enable one to identify and isolate neurons from a population cells.
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.