Abstract: Provided herein are methods and compositions to determine the efficacy of a nucleic acid pre-amplification reaction.

Abstract: Emulsion compositions are provided herein. Also provided herein are kits containing one or more emulsion compositions or components for making such emulsion compositions. Also provided herein are methods of using such emulsion compositions, such as for amplification of target nucleic acids in emulsion droplets.

Abstract: System, including methods and apparatus, for spacing droplets from each other and for detection of spaced droplets.

Abstract: The present disclosure provides methods and systems for amplifying and analyzing nucleic acid samples. The present disclosure provides methods for preparing cDNA and/or DNA molecules and cDNA and/or DNA libraries using modified reverse transcriptases.

Abstract: Methods and compositions for detecting genetic instability using digital amplification assays. The methods may be performed in a set of isolated volumes and generally may involve competitive hybridization of a competitor and a probe/primer with a normal allele and one or more mutant alleles of a microsatellite locus. The competitor may be configured to compete similarly with, or to outcompete, the primer/probe for hybridization with the normal allele. The primer/probe may be configured to outcompete the competitor for hybridization with various mutant alleles of the locus that alter the length of the repetitive sequence by different amounts. Isolated volumes in which the primer/probe outcompetes the competitor may be enumerated, and represent one or more of the mutant alleles. The methods may enable diagnosing microsatellite instability and treating a subject based on the diagnosis.

Abstract: Methods of generating a nucleic acid signature for identifying particles associated in a partition are provided. In one aspect, the method comprises: partitioning a sample into a plurality of partitions comprising a particle comprising a solid support surface, the solid support surface having a plurality of oligonucleotide primers conjugated thereon, wherein the oligonucleotide primers comprise a barcode sequence, and wherein the partitions have 0, 1, or more than 1 particles per partition; providing in a partition a substrate comprising a barcode sequence or repeating clonal barcode sequences; and in the partition, associating a first particle conjugated to oligonucleotide primers comprising a first barcode sequence and a second particle conjugated to oligonucleotide primers comprising a second barcode sequence to a barcode sequence from the substrate, thereby generating a nucleic acid signature for the particles in the partition.

Abstract: Methods and devices for transferring materials between containers are discussed. One such connector includes: a base; a first elongate structure having first and second ends, the first elongate structure extending from a first side of the base at the first end to the second end distal the base, the second end forming a first opening sized and configured to receive a first container; a duct extending through the base and having a first tip skirted on one or more sides by the first elongate structure; a first guard positioned within the first elongate structure, wherein the first guard comprises a first surface, and the first surface is located further away from the base than the first tip. When the first container is moved into the first opening, the first surface moves toward the base, and the first tip enters the first container, creating a fluid path for the first container.

Abstract: System, including methods, apparatus, and compositions, for performing amplification assays with an amplification reporter including a first oligomer and a second oligomer capable of base-pairing with one another below a melting temperature of the reporter. The reporter may have a detectable photoluminescence that is affected, such as reduced, by base-pairing of the first and second oligomers with one another. A target, such as a nucleic acid target sequence, may be amplified in at least one volume, such as a plurality of partitions, above the melting temperature, and photoluminescence of the reporter may be detected from the at least one volume below the melting temperature. A property of the target, such as a concentration of the target, may be determined based on the photoluminescence detected.

Abstract: The invention generally relates to methods for forming mixed droplets. In certain embodiments, methods of the invention involve forming a droplet, and contacting the droplet with a fluid stream, wherein a portion of the fluid stream integrates with the droplet to form a mixed droplet.

Abstract: Methods of, and compositions for, analysis using digital amplification assays with unconventional/inverse changes in photoluminescence to indicate the presence of one or more targets. In an exemplary method, isolated volumes may be formed, only a subset of which contain a target. Each volume may include a probe having a label, a sink having a quencher and configured to hybridize with the probe to quench the label, and a separator configured to hybridize with the probe and/or the sink to block hybridization of the sink with the probe. An amplification reaction may be performed in the volumes to generate an amplicon corresponding to the target. The separator may hybridize with the amplicon, and may be extended or degraded by the amplification reaction. Photoluminescence of the label may be detected from the volumes, and the photoluminescence of target-positive volumes may be less than that of target-negative volumes.

Abstract: A cell capture system including an array, an inlet manifold, and an outlet manifold. The array includes a plurality of parallel pores, each pore including a chamber and a pore channel, an inlet channel fluidly connected to the chambers of the pores; an outlet channel fluidly connected to the pore channels of the pores. The inlet manifold is fluidly connected to the inlet channel, and the outlet channel is fluidly connected to the outlet channel. A cell removal tool is also disclosed, wherein the cell removal tool is configured to remove a captured cell from a pore chamber.

Abstract: System for performing a flow-based assay. The system may comprise a droplet generator to produce an emulsion including droplets in a carrier fluid. The system also may comprise a thermocycler including two or more temperature-controlled zones and also including a channel connected to the droplet generator for receiving the emulsion. The channel may form a single-pass continuous fluid route traversing the temperature-controlled zones multiple times, such that droplets passing through the channel are thermally cycled. The system further may comprise a detection station downstream from the thermocycler and configured to detect a signal from the droplets after such droplets have been thermally cycled by passing through the channel.

Abstract: System, including methods and apparatus, for optical detection. The system may comprise a light source to generate a beam of light, an optical element including a light guide and an exit window, and at least one detector.

Abstract: Methods of detecting or quantifying short RNA or DNA molecules using split cycle amplification are provided.

Abstract: System, including methods, apparatus, compositions, and kits, for making and using a stabilized emulsion. A method of generating a stabilized emulsion is provided. In the method, an aqueous phase may be provided. The aqueous phase may include an effective concentration of one or more skin-forming proteins. An emulsion may be formed. The emulsion may include droplets of a dispersed phase disposed in a continuous phase, with the aqueous phase being the continuous phase or the dispersed phase. The emulsion may be heated to create an interfacial skin between each droplet and the continuous phase, to transform the droplets into capsules.

Abstract: A system and method for isolating and analyzing single cells, comprising: a substrate having a broad surface; a set of wells defined at the broad surface of the substrate, and a set of channels, defined by the wall, that fluidly couple each well to at least one adjacent well in the set of wells; and fluid delivery module defining an inlet and comprising a plate, removably coupled to the substrate, the plate defining a recessed region fluidly connected to the inlet and facing the broad surface of the substrate, the fluid delivery module comprising a cell capture mode.

Abstract: Methods, libraries, and kits for nucleotide sequencing are provided. For example, methods can comprise providing a plurality of partitions, the partitions comprising a set of two or more different primers and a target nucleic acid, wherein different partitions contain different sets of primers with a majority of primers in the sets being common with a different primer set but wherein any two different partitions having a common primer contain no more than one common primer; and hybridizing the target nucleic acid to the primers in the reaction partitions under conditions in which fully complementary primers hybridize to the target sequence and primers that are not fully complementary do not hybridize to the target nucleic acid.

Abstract: Microfluidic systems and methods for arranging a set of objects. In an exemplary method, the set of objects may be transported in carrier fluid along a microfluidic channel structure having a reformatting zone including an object-accessible region and at least one object-excluding region. A portion of the carrier fluid may be moved from the object-accessible region to the at least one object-excluding region in an upstream section of the reformatting zone, to reduce a spacing of objects of the set. The portion of the carrier fluid may be directed into the object-accessible region from the at least one object-excluding region in a downstream section of the reformatting zone, to increase a spacing of objects of the set. The steps of moving and directing in combination may increase the spacing between objects disproportionately for a subset of the objects that are closest to one another.

Abstract: A combination imaging system includes a housing having a base and a lid, the lid having a closed position against the base and having an open position. The imaging device further includes a contact area image sensor. The lid shields the contact area image sensor from ambient light when the lid is in the closed position. The imaging device also includes a camera. The camera includes a lens, and the field of view of the camera encompasses at least a portion of an imaging area of the contact area image sensor when the lid is in the open position. The device may be especially useful for capturing a chemiluminescent image of an electrophoretic assay result, and capturing a colorimetric image of the same result, so that non-chemiluminescent protein standards may be located with respect to chemiluminescent analytes of interest.

Abstract: Method of analysis. In the method, a first emulsion and a second emulsion substantially separated from one another by a spacer fluid may be formed. The first emulsion, the spacer fluid, and the second emulsion may be flowed in a channel from a fluid inlet to a fluid outlet of a heating and cooling station having two or more temperature-controlled zones, such that each emulsion is thermally cycled to promote amplification of a nucleic acid target in droplets of the emulsion. Amplification data may be collected from individual droplets of each emulsion downstream of the heating and cooling station. A level of the nucleic acid target present in each emulsion may be determined based on the amplification data collected from the individual droplets of the emulsion.