Abstract: The technology relates in part to methods and compositions for detecting oncogenic structural variants.

Abstract: In some aspects, the present disclosure generally relates to methods and compositions for detecting a plurality of molecules of one or more analytes in a sample. In some aspects, the present disclosure relates to methods for determining the locations and identities of analytes in a biological sample using detectable probes. In some aspects, the present disclosure relates to methods for reducing the crowding of signals that are used for determining the locations of the analytes (e.g., spot-calling signals). The methods herein have particular applicability in the detection of spot-calling signals and barcode sequences in sequencing-by-hybridization (SBH) methods, including those relying on combinatorial labeling schemes and decoding of the barcodes by sequential cycles of spot-calling and/or decoding using hybridization probes.

Abstract: The present disclosure relates in some aspects to methods, systems, and kits for analyzing a biological sample comprising generating a rolling circle amplification product (RCP) using a target ribonucleic acid (RNA) as a primer. In some aspects, RNase H and a nucleic acid oligonucleotide are used to generate a free 3? end of the target RNA to prime RCA.

Abstract: The present disclosure provides methods and processes for increasing the efficiency and accuracy of nucleic acid sequencing using techniques such as polymerase chain reaction (PCR). The methods described herein can be used to achieve clonal amplification even with a greater than Poisson distribution of beads and/or nucleic acid templates into an emulsion. A PCR method may comprise generating a partition (e.g., a droplet) comprising at least two beads and/or at least two nucleic acid molecules and generating clonal amplification products corresponding to the nucleic acid molecule, at least a subset of which may be attached to a bead.

Abstract: The present disclosure relates to materials and methods for spatially analyzing nucleic acids that have been fragmented with a transposase enzyme, alone or in combination with other types of analytes.

Abstract: A plasmid developed for the production of recombinant protein in mammalian cells is provided. The plasmid vector includes the nucleic acid sequence with at least 80% similarity to SEQ ID NO: 1. The plasmid vector includes a CMV promoter, a CMV enhancer, CMV intron A, SV40 small t antigen intron, SV40 poly(A) signal, Syn21, and an hTERT-SV40 enhancer.

Abstract: The present invention relates to a combination therapy a CHEK1 inhibitor and a TOP1 inhibitor for use in a method of treatment of colorectal cancer in a patient.

Abstract: The invention generally relates to sequencing library preparation methods. In certain embodiments, two or more template nucleic acids are joined together by a linking molecule, such as a PEG derivative. Identical copies of a nucleic acid fragment or both strands of a duplex fragment may be linked together. The linked nucleic acids are amplified, creating linked amplicons. Emulsion PCR with linked primers creates linked template nucleic acids for seeding sequencing clusters and errors can be readily identified by their presence on only one of the linked fragments.

Abstract: A substrate holder includes a base configured to receive a substrate; a cover configured to mateably engage with the base, the cover defining an opening formed by inner sidewalls; and a removable insert defining a surface, the removable insert being configured to be received within the opening of the cover. The removable insert includes a gasket; a projection coupled to the gasket; and at least two insert tabs extending from opposite sides of the removable insert, each insert tab being configured to engage with at least one of the inner sidewalls forming the opening of the cover.

Abstract: A portable incubator system integrated to a mobile phone providing a real-time tracking of samples and data flow is provided. The portable incubator system allowing cells to be cultured, reproduced and characterized in real-time without a need for a commercial incubator and a microscope-camera system installed within the portable incubator system.

Abstract: Disclosed herein are methods of amplifying an analyte in a biological sample using a bridging oligonucleotide that hybridizes to a captured analyte. The methods disclosed herein include steps of (a) contacting a biological sample with a substrate having capture probes comprising a capture domain and a spatial barcode; (b) hybridizing the analyte to the capture domain; and (c) contacting the analyte to a bridging oligonucleotide comprising (i) a capture-probe-binding sequence, and (ii) an analyte-binding sequence; (d) extending the bridging oligonucleotide; and (e) determining (i) all or a part of the sequence of the analyte, or a complement thereof, and (ii) the spatial barcode, or a complement thereof, and using the determined sequence of (i) and (ii) to determine the location of the analyte in the biological sample.

Abstract: A sample holder includes a first member featuring a first retaining mechanism configured to retain a first substrate that includes a sample, a second member featuring a second retaining mechanism configured to retain a second substrate that includes a reagent medium, and an alignment mechanism connected to at least one of the first and second members, and configured to align the first and second members such that the sample contacts at least a portion of the reagent medium when the first and second members are aligned.

Abstract: Provided herein are materials and methods for in situ labeling of a biological sample for use in spatial analysis of one or more analytes in the biological sample. In some aspects, in situ labeling of a biological sample includes labeling the biological sample with one or more spatial barcodes.

Abstract: Recognized herein is the need for methods and processes for increasing the efficiency and accuracy of paired end sequencing.

Abstract: Systems are provided for detecting and quantitating short nucleic acid molecules.

Abstract: Provided herein are methods, compositions, and kits for the spatial analysis of target nucleic acids, or complements thereof, by their 5? end.

Abstract: The present disclosure relates to materials and methods for spatially analyzing nucleic acids that have been fragmented with a transposase enzyme, alone or in combination with other types of analytes.

Abstract: Devices, systems, and their methods of use, for generating and collecting droplets are provided. The device includes a collection region comprising a side wall canted at an angle. The invention further provides multiplex devices that increase droplet formation.

Abstract: Disclosed are systems and methods for selecting biological particles (e.g., cells or nuclei) based on specific binding to a substrate and single-biological particle measurement of analytes from the substrate-bound biological particles (e.g., cells or nuclei). Single biological particles (e.g., cells or nuclei) from a population of biological particles are captured through their binding to biological particle- (e.g., cell- or nucleus-) and/or molecule-specific biological particle (e.g., cell or nucleus) capture moieties on a substrate. Analytes are released from the single captured biological particles (e.g., cells or nuclei) and bind to analyte-specific barcode molecules associated with the specific biological particle (e.g., cell or nucleus) capture moieties to which a biological particle (e.g., a cell or nucleus) has bound. Analysis of the barcode molecules identifies the bound analytes.

Abstract: Embodiments of the invention provide a method of treating cancer, the method comprising providing a subject having cancer cells, and contacting the cancer cells with a therapeutically effective amount of a G2/M checkpoint inhibitor. Embodiments of the invention also provide a method of treating cancer in a subject, the method comprising the steps of: (a) receiving a sample of the cancer cells from the subject; (b) determining if at least a portion of the sample of the cancer cells is LKB1 deficient; and (c) contacting the cancer cells with a therapeutically effective amount of a G2/M checkpoint inhibitor. Embodiments of the invention also provide a method of treating cancer in a subject, the method comprising contacting the cancer cells with a therapeutically effective amount of a Wee1 inhibitor and a therapeutically effective amount of a second pharmaceutical composition.