Abstract: The present disclosure provides methods, compositions, kits, and systems useful in the determination and evaluation of the immune repertoire. In one aspect, methods provide for determining convergence of T cell receptor beta and T cell receptor gamma repertoires in samples prior to a treatment and predicting a subject's response to the treatment. In another aspect, methods provide predicting a subject's potential or predisposition to be protected from or vulnerable to an adverse event following a treatment.

Abstract: According to various embodiments, a method is provided that comprises washing an array of DNA-coated beads on a substrate, with a wash solution to remove stacked beads from the substrate. The wash solution can include inert solid beads in a carrier. The DNA-coated beads can have an average diameter and the solid beads in the wash solution can have an average diameter that is at least twice the diameter of the DNA-coated beads. The washing can form dislodged DNA-coated beads and a monolayer of DNA-coated beads. In some embodiments, first beads for forming an array are contacted with a poly(ethylene glycol) (PEG) solution comprising a PEG having a molecular weight of about 350 Da or less. In some embodiments, slides for forming bead arrays are provided as are systems for imaging the same.

Abstract: A system for separating biological molecules includes a plurality of capillaries, a capillary mount, a plurality of optical fibers, a fiber mount, an optical detector, and a motion stage. The plurality of capillaries are configured to separate biological molecules in a sample. Each capillary comprising a detection portion configured to pass electromagnetic radiation into the capillary. The plurality of capillaries are coupled to the capillary mount such that the detection portions are fixedly located relative to one another. Each optical fiber includes a receiving end to receive emissions. The optical fibers are coupled to the fiber mount such that the receiving ends of the optical fibers are fixedly located relative to one another. The optical detector is configured to produce an alignment signal. The motion stage is configured to align the receiving ends of the optical fibers to the detection portions based on values of the alignment signal.

Abstract: Provided are systems and methods that allow for brightfield imaging in a flow cytometer, allowing for collection of fluorescence and high-quality image date. The disclosed technology also gives rise to an illumination pattern that allows a user to create different oblique or structured illumination profiles within a static system. With the disclosed approach, a user can illuminate a sample from a first direction (e.g., with laser illumination configured to give rise to one or more of fluorescence information and scattering information), collect scattering information from a second direction, collect fluorescence information from a third direction, and capture an image of the sample from a fourth direction. (Two or more of the foregoing can be accomplished simultaneously.) Also as described elsewhere herein, an illumination used to illuminate the sample for visual image capture can be communicated to the same through a lens that also collects fluorescence from the sample.

Abstract: The present set of embodiments relate to a system, method, and apparatus for culturing cells within a cell culture vessel having a mixing element. The cell culture system includes a flexible portion and a mixing element disposed therein. The mixing element includes a suspended foldable portion. The system is configured to reduce shear stress on cells without compromising mixing efficiency. This reduction is accomplished by using a mixing element having a large surface area allowing for reduced rotational speeds. The system is collapsible for ease of transport and disposal. The flexible portion collapses and the foldable portion folds to minimize the volume of the system while not in operation.

Abstract: A method for processing a fluid includes removably securing a retention member to a vessel that bounds a chamber; inserting a collapsible bag within the chamber of the vessel; securing the bag to the retention member so that the bag is supported within the chamber of the vessel; and dispensing a fluid into a compartment of the collapsible bag supported within the chamber of the vessel. The fluid can be mixed within bag while the bag is disposed within the vessel.

Abstract: The present disclosure is directed to compositions, methods and kits for amplifying target nucleic acids while reducing non-specific amplification and undesired amplification products using a dual hot start reaction mixture that comprise at least two different hot start mechanisms.

Abstract: Methods and systems for generating a computer-implemented interactive graphical user interface for facilitating finding appropriate antibody products utilizing visual evaluation of sequence information are disclosed. An antibody product listing within the graphical user interface is generated. The antibody product listing is responsive to a user interaction. The antibody product listing includes at least one antibody product including corresponding sequence information and product specifications. A sequence infographic is generated based on the corresponding sequence information, wherein the sequence infographic includes an amino acid sequence area of interest indicator. The sequence infographic is displayed aligned relative to a plurality of sequence infographics.

Abstract: A sensor component includes a sensor including a sensor surface and a reaction site in cooperation with the sensor and exposing the sensor surface. The reaction site including a reaction site surface. A surface agent is bound to the reaction site surface or the sensor surface. The surface agent includes a surface active functional group reactive with Bronsted base or Lewis acid functionality on the reaction site surface or the sensor surface and including distal functionality that does not have a donor electron pair.

Abstract: In some embodiments, the disclosure relates generally to compositions, comprising a single reaction mixture containing a plurality of different populations of discrete supports, and a plurality of different populations of target nucleic acids. The single reaction mixture can contain a first population of beads; a second population of beads; a first population of target nucleic acids, where at least two different target nucleic acids in the first population of target nucleic acids can bind to a bead in the first population of beads; and a second population of target nucleic acids, where at least two different target nucleic acids in the second population of target nucleic acids can bind to a bead in the second population of beads. The single reaction mixture can be employed to monoclonally amplify the first target nucleic acids on the first beads, and monoclonally amplify the second target nucleic acids on the second beads.

Abstract: In one embodiment, a device is described. The device includes a material defining a reaction region. The device also includes a plurality of chemically-sensitive field effect transistors have a common floating gate in communication with the reaction region. The device also includes a circuit to obtain respective output signals from the chemically-sensitive field effect transistors indicating an analyte within the reaction region.

Abstract: A method for nucleic acid sequencing includes receiving nucleic acid sequencing data from a sequencing instrument that receives and processes a sample nucleic acid in a sequencing-by-synthesis process. The method also includes generating a set of candidate sequences of bases for the observed or measured nucleic acid sequencing data by determining a predicted signal for candidate sequences using a simulation framework. The simulation framework incorporates an estimated carry forward rate (CFR), an estimated incomplete extension rate (IER), an estimated droop rate (DR), an estimated reactivated molecules rate (RMR), and an estimated termination failure rate (TFR), the RMR being greater than or equal to zero and the TFR being lesser than one. The method also includes identifying, from the set of candidate sequences of bases, a candidate sequence as corresponding to the sequence for the sample nucleic acid.

Abstract: A method, computer program product, and system are provided to calibrate a sensor array with a plurality of sensors. The method can include sweeping a voltage of a reference electrode from a first voltage to a second voltage, where the reference electrode is in fluid communication with the sensor array. The output voltage of each of the plurality of sensors can be monitored at one or more voltages within the first and second voltages. An overall average gain of the plurality of sensors can be calculated at each of the one or more voltages. Further, an acquisition window for the sensor array can be determined. The acquisition window can include a maximum distribution of sensors that provides a maximal overall average gain at a particular reference electrode voltage.

Abstract: Provided herein are compounds, compositions, kits, uses, and methods for assessing the viability of cells and/or quantifying the amount of live and dead cells in a mixture using differential stains. In some embodiments, the compounds are used in culture media or can function independently of fixation and/or permeabilization. In some embodiments, the compounds comprise a platinum atom. In some embodiments, the compounds comprise a nitrogen mustard moiety.

Abstract: A temperature insulated packaging system includes a container having interior surface bounding an interior volume and a liner disposed within the interior volume and at least partially bounding a compartment configured to receive an item for temperature insulated shipping. The liner includes a first sleeve made of cellulose material and at least partially bounds a channel. The first sleeve has an outside wall disposed adjacent to the container and an opposing inside wall disposed adjacent to the compartment configured to receive the item for shipping, the channel being disposed between the inside wall and the outside wall. At least one insulation sheet is disposed within the channel of the first sleeve, the at least one insulation sheet being made of a cellulose material and having a plurality of recesses formed thereon.

Abstract: In one aspect, a biological sequencing device comprising a cartridge configured to be removed from the instrument is disclosed. In various embodiments the cartridge can include one or more capillaries suitable for capillary electrophoresis, a reservoir and a pump. In various embodiments the reservoir can contain a separation matrix. In various embodiments the pump can load a capillary with separation matrix. In another aspect the biological sequencing device can include one or more capillaries and an integrated valve assembly. In various embodiments the integrated valve assembly can provide a polymer to the one or more capillaries.

Abstract: A liquid mixing system includes a support housing at least partially bounding a compartment. A mount is secured to the support housing. A drive motor assembly is configured to engage a drive shaft for moving the drive shaft within the compartment of the support housing. A four bar linkage system extends between the mount and the drive motor assembly, the four bar linkage system being movable between a first position wherein the drive motor assembly is disposed at a first elevation and a second position wherein the drive motor assembly is disposed at a second elevation that is different from the first elevation.

Abstract: Systems and method for identifying variants associated with a genetic disease can include obtaining calls for a plurality of individuals for a list of variant positions. The calls can be compared to identify variants that are found in affected individuals and absent in non-affected individuals. Such variants can include loss of heterozygosity, trans-phased compound heterozygotes, increased frequency mitochondrial variants, homozygous recessive variants, de novo variants, sex-linked variants, and combinations thereof.

Abstract: The disclosure provides gene fusions, gene variants, and novel associations with disease states, as well as kits, probes, and methods of using the same.