Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and analyte characterization. Such polynucleotide processing may be useful for a variety of applications, including analyte characterization by polynucleotide sequencing. The compositions, methods, systems, and devices disclosed herein generally describe barcoded oligonucleotides, which can be bound to a bead, such as a gel bead, useful for characterizing one or more analytes including, for example, protein (e.g., cell surface or intracellular proteins), genomic DNA, and RNA (e.g., mRNA or CRISPR guide RNAs). Also described herein, are barcoded labelling agents and oligonucleotide molecules useful for “tagging” analytes for characterization.

Abstract: A microfluidic system includes a microfluidic chip having a plurality of fluid channels, each fluid channel having an opening providing access to an interior of the fluid channel, and a gasket disposable on the microfluidic chip in an aligned configuration, the gasket including a first side configured to face the microfluidic chip in the aligned configuration, a second side opposite the first side, and an aperture extending through the gasket from the first side to the second side, the aperture being sized and positioned to allow a communication of pressure from the second side of the gasket to the openings of at least two fluid channels when the gasket is in the aligned configuration.

Abstract: Methods and systems are provided for sample preparation techniques and sequencing of macromolecular constituents of cells and other biological materials.

Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and analyte characterization. Such polynucleotide processing may be useful for a variety of applications, including analyte characterization by polynucleotide sequencing. The compositions, methods, systems, and devices disclosed herein generally describe barcoded oligonucleotides, which can be bound to a bead, such as a gel bead, useful for characterizing one or more analytes including, for example, protein (e.g., cell surface or intracellular proteins), genomic DNA, and RNA (e.g., mRNA or CRISPR guide RNAs). Also described herein, are barcoded labelling agents and oligonucleotide molecules useful for “tagging” analytes for characterization.

Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and analyte characterization. Such polynucleotide processing may be useful for a variety of applications, including analyte characterization by polynucleotide sequencing. The compositions, methods, systems, and devices disclosed herein generally describe barcoded oligonucleotides, which can be bound to a bead, such as a gel bead, useful for characterizing one or more analytes including, for example, protein (e.g., cell surface or intracellular proteins), genomic DNA, and RNA (e.g., mRNA or CRISPR guide RNAs). Also described herein, are barcoded labelling agents and oligonucleotide molecules useful for “tagging” analytes for characterization.

Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and antigen screening. Polynucleotide processing may be useful for a variety of applications. Antigen screening may comprise the use of one or more engineered cells. Engineered cells may be useful for characterizing one or more analytes including, for example, a polypeptide antigen.

Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and analyte characterization from a single cell. Such polynucleotide processing may be useful for a variety of applications. The compositions, methods, systems, and devices disclosed herein generally describe barcoded oligonucleotides, which can be bound to a bead, such as a gel bead, useful for characterizing one or more analytes including, for example, protein (e.g., cell surface or intracellular proteins), genomic DNA, epigenetic information (e.g., accessible chromatin, DNA methylation), and RNA molecules (e.g., mRNA or CRISPR guide RNAs). In some cases, the disclosed methods comprise analysis of analytes from a cell using a cell bead.

Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and analyte characterization from one or more cells. Such polynucleotide processing may be useful for a variety of applications, including characterization of major histocompatibility complex (MHC) molecules. The compositions, methods, systems, and devices disclosed herein generally describe peptides and barcoded oligonucleotides, which can be bound to a bead, such as a gel bead, useful for characterizing MHC molecules from one or more cells.

Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and analyte characterization from a single cell. Such polynucleotide processing may be useful for a variety of applications. The compositions, methods, systems, and devices disclosed herein generally describe barcoded oligonucleotides, which can be bound to a bead, such as a gel bead, useful for characterizing one or more analytes including, for example, protein (e.g., cell surface or intracellular proteins) and chromatin (e.g., accessible chromatin).

Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and analyte characterization from a single cell. Such polynucleotide processing may be useful for a variety of applications, including cell lineage analysis. Cell lineage analysis may comprise the use of one or more lineage tracing nucleic acid molecules. The disclosed methods may comprise using a lineage tracing nucleic acid molecule to identify a biological particle with one or more progenitor cells.

Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and analyte characterization from one or more cells. Such polynucleotide processing may be useful for a variety of applications, including generation of labeled macromolecules, including major mistocompatability complex (MHC) molecules, dextramers, etc. Labeled macromolecules may be generated using an in vitro transcription reaction. Labeled macromolecules may be generated in one or more partitions.

Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and analyte characterization. Such polynucleotide processing may be useful for a variety of applications, including analyte characterization by polynucleotide sequencing. The compositions, methods, systems, and devices disclosed herein generally describe barcoded oligonucleotides, which can be bound to a bead, such as a gel bead, useful for characterizing one or more analytes including, for example, protein (e.g., cell surface or intracellular proteins), genomic DNA, and RNA (e.g., mRNA or CRISPR guide RNAs). Also described herein, are barcoded labelling agents and oligonucleotide molecules useful for “tagging” analytes for characterization.

Abstract: Methods and systems are provided for sample preparation techniques and sequencing of macromolecular constituents of cells and other biological materials.

Abstract: A microfluidic emulsion droplet generation system and methods of use thereof are provided. The system may include a microfluidic substrate having a flow path configured and arranged for emulsion droplet generation, at least one textured surface in the flow path configured and arranged for inducing surface-mediated coalescence of emulsion droplets; and at least one channel junction in the flow path for emulsion droplet formation.

Abstract: Microfluidic channels networks and systems are provided. One network includes a first fluid channel having a first depth dimension; at least a second channel intersecting the first channel at a first intersection; at least a third channel in fluid communication with the first intersection, at least one of the first intersection and the third channel having a depth dimension that is greater than the first depth dimension. Also provided is a flow control system for directing fluids in the network. Systems are additionally provided for flowing disrupted particles into a droplet formation junction, whereby a portion of the disrupted particles or the contents thereof are encapsulated into one or more droplets. Further provided is a method for controlling filling of a microfluidic network by controlling passive valving microfluidic channel network features.

Abstract: A microfluidic system for manipulating particles in a fluid is provided. The system includes a microfluidic chip having at least one channel and at least one filter feature, wherein the filter feature includes a field of physical obstacles configured and arranged to remove physical contaminants associated with the particles. The filter features are particularly suited to remove contaminants associated with gel beads manipulated by microfluidic handling.

Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing.

Abstract: The present disclosure provides methods and systems for nucleic acid processing. A method for preparing a sequencing set may include providing a template nucleic acid and amplifying the template nucleic acid to provide a complementary nucleic acid. Next, the complementary nucleic acid may be fragmented and barcoded to produce a first set of barcoded fragments comprising a plurality of first barcoded fragments. Next, the plurality of first barcoded fragments may be fragmented to yield a second set of barcoded fragments comprising a plurality of second barcoded fragments.

Abstract: Methods and systems are provided for sample preparation techniques and sequencing of macromolecular constituents of cells and other biological materials.

Abstract: The invention provides devices, systems, and methods for extracting target objects from a sample. In the method, a stream of sample containing a plurality of target and non-target objects is directed by first and second streams of buffer through a sample inlet channel into a fluid junction and through the fluid junction into a sample waste channel. In response to detecting a target object within the stream of sample, an actuator is energized to close a normally open valve, resulting in a transient burst of cross-flow into the fluid junction that briefly diverts the flow of sample within the fluid junction and results in an aliquot of sample being directed into an aliquot delivery channel. The combination of the valve and the actuator acts as a self-limiting pulse generator.