Abstract: Compositions, kits and methods are described that comprise one or more constructs, each construct comprising a ligand attached or conjugated to a polymer construct, e.g., an oligonucleotide sequence, by a linker, each ligand binding specifically to a single target located in or on the surface of a cell. The polymer construct comprises a) an Amplification Handle; b) a Barcode that specifically identifies a single ligand; c) an optional Unique Molecular Identifier that is positioned adjacent to the Barcode on its 5? or 3? end; and d) an Anchor for hybridizing to a complementary sequence, e.g., for generation of a double-stranded oligonucleotide. These compositions are used in methods, including high throughput methods, for detecting one or more targets or epitopes in a biological sample. These compositions are also used in a high throughput method for characterizing a cell by simultaneous detection of one or more epitopes located in or on the cell and its transcriptome.

Abstract: Embodiments of the invention provide an improved biosensor for biological or chemical analysis. According to embodiments of the invention, backside illumination (BSI) complementary metal-oxide-semiconductor (CMOS) image sensors can be used to effectively analyze and measure fluorescence or chemiluminescence of a sample. This measured value can be used to help identify a sample. Embodiments of the invention also provide methods of manufacturing an improved biosensor for biological or chemical analysis and systems and methods of DNA sequencing.

Abstract: The present invention provides a composition comprising a plurality of labeled neurons, each of which is labeled by an expression construct that encodes a unique barcoded nucleic acid.

Abstract: Provided are methods of producing size-selected nucleic acid libraries. The methods include contacting a nucleic acid sample and a nucleic acid binding reagent including an affinity tag, under conditions in which nucleic acids of less than a desired length are substantially bound to the nucleic acid binding reagent and nucleic acids of the desired length are substantially not bound to the nucleic acid binding reagent. The conditions include the duration of the contacting, the concentration of the nucleic acid binding reagent, or both. The methods further include separating, using the affinity tag, the nucleic acids of less than the desired length bound to the nucleic acid binding reagent from the nucleic acids of the desired length not bound to the nucleic acid binding reagent, to produce a size-selected nucleic acid library. Compositions and kits that find use, e.g., in practicing the methods of the present disclosure, are also provided.

Abstract: Disclosed is a method of fragmenting DNA comprising contacting a sample of target DNA with (a) a composition comprising an active transpososome, and (b) a composition comprising an inactive transpososome, under conditions suitable for transpososome activity, wherein a ratio of an amount of the inactive transpososome in the composition of (b) to an amount of the active transpososome in the composition of (a) determines the mean fragment size and a level of insertion bias.

Abstract: A method for controlled production of an array of planar microparticles with the multiplexing of molecules on the surface thereof, intended to function as molecular sensors and/or actuators and a matrix (array) of microparticles, the surface thereof being printed with all of the molecular components required to provide the surface with functionality. Different molecular elements are multiplexed on the surface of each particle while they are supported on a substrate by means of a structural foot engraved below the particle. These microparticles can be released mechanically from the support on which they are produced using a controlled mechanical rupture method which is not chemically aggressive and therefore does not affect the molecules previously printed on the surface. The array and the particles contained therein offer great versatility in both chemical and/or biological applications.

Abstract: This invention provides methods for the screening and identification of antigenic components in a tissue or organ of interest.

Abstract: Embodiments provided herein relate to methods and compositions for preparing an immobilized library of barcoded DNA fragments of a target nucleic acid, identifying genomic variants, determining the contiguity information, phasing information, and methylation status of the target nucleic acid.

Abstract: The present disclosure relates to multifunctional verification molecules, including molecules according to formula (I): G-L-(B)K-Q-U, wherein G, L, B, K, Q, and U are defined herein. The present disclosure also relates to methods of preparing and using such multifunctional verification molecules to remove defective multifunctional molecules and to quantify synthetic yield.

Abstract: Provided are a protein complex in which estrogen receptor 2 (-ERT2) is fused to CRISPR associated protein 9 (Cas9), and a recombinant vector carrying a gene coding the protein complex, wherein ERT2 is bonded to the N-terminus and C-terminus of nuclear localization sequence (NLS)-removed Cas9 and the complex has the advantage of translocating from the cytosol into the nucleus at a certain time point upon treatment with tamoxifen and modifying a specific DNA with the aid of guide RNA (gRNA), ultimately enabling a more elaborate DNA modification operation in a desired part at a desired time point.

Abstract: Provided herein is a method for manufacturing a microarray system, for example, 3-dimensional lattice microarray system, for DNA sequence detection and analysis. A solid support, such as a plastic substrate, is contacted with a formulation containing a plurality of nucleic acid probes, a plurality of bifunctional polymer linkers, such as oligothymidine linkers, and a solvent mixture of water and a water-miscible liquid. The bifunctional polymer linkers are attached to the solid support and the water is evaporated. Then the nucleic acid probes are attached to the bifunctional polymer linker.

Abstract: Disclosed herein are methods for tracking solutions, (e.g., reaction conditions in solutions). In some embodiments, the method comprises: contacting a first lanthanide-chelator complex to a first solution to generate a first barcoded solution, wherein the first lanthanide-chelator complex comprises a first lanthanide chelated by a first chelator; contacting a second lanthanide-chelator complex to a second solution to generate a second barcoded solution, wherein the second lanthanide-chelator complex comprises a second lanthanide chelated by a second chelator; mixing the first barcoded solution and the second barcoded solution to form one or more mixtures; and identifying the first lanthanide ions in the mass spectrum and the second lanthanide ions in the mass spectrum to track the condition of each of the one or more mixtures.

Abstract: Provided are an improved genome editing system and a method that has high specificity, which are capable of obtaining stable mutation types. The system includes an expression construct including a coding sequence of a gRNA targeting at least one genomic target sequence; an expression construct including a coding sequence of a CRISPR nuclease; and an expression construct including a coding sequence for a gRNA targeting a target sequence within the coding sequence of the CRISPR nuclease. Upon introduction into the cell, the gRNA targeting the at least one genomic target sequence directs the CRISPR nuclease to the at least one genomic target sequence and results in one or more mutations in the genomic target sequence, and the gRNA targeting a target sequence within the coding sequence of the CRISPR nuclease directs the CRISPR nuclease to the target sequence within the coding sequence of the CRISPR nuclease and results in an inactivating mutation of the CRISPR nuclease.

Abstract: The present invention relates to libraries of phosphopeptide-encoding oligonucleotides and methods of preparing such libraries. The present invention also relates to methods of detecting, visualizing, or screening for phosphorylation-dependent protein-protein interactions using recombinant phosphopeptides and/or phosphopeptide-encoding oligonucleotides. The present invention also relates to sets or kits of oligonucleotides having regions that encode phosphopeptides.

Abstract: Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations.

Abstract: A population of nucleic acid adaptors is provided. In some embodiments, the population contains at least 50,000 different molecular barcode sequences, where the barcode sequences are double-stranded and at least 90% of the barcode sequences have an edit distance of at least 2. In certain cases, the adaptor may have an end in which the top and bottom strands are not complementary (i.e., may be in the form of a Y-adaptor). In some embodiments and depending on the how the adaptor is going to be employed, the other end of the adaptor may have a ligatable end or may be a transposon end sequence.

Abstract: The present invention relates to novel fluorophores and their use in combination with novel nucleic acid molecules, called aptamers, that bind specifically to the fluorophore and thereby enhance the fluorescence signal of the fluorophore upon exposure to radiation of suitable wavelength. Molecular complexes formed between the novel fluorophores, novel nucleic acid molecules, and their target molecules are described, and the use of multivalent aptamer constructs as fluorescent sensors for target molecules of interest are also described.

Abstract: Aspects of the invention include methods for preparing sequencing libraries, performing sequencing procedures that can correct for process-related errors, and identifying rare variants that are or may be indicative of cancer.

Abstract: Provided herein is a 3-dimensional lattice microarray system for DNA sequence detection and analysis. The system has a plurality of bifunctional polymer linkers, on one end of which are attached nucleic acid probes where each have a sequence complementary to signature nucleotide sequences in pathogens, plants or animals. The other end of the bifunctional polymer linker is attached to a solid support by non-covalent or covalent means. Each of the nucleic acid probes have terminal thymidine bases at the 5? and 3? ends that permit attachment of the probes to the bifunctional polymer linkers. Also provided is a method for fabricating the microarray system by first attaching the bifunctional polymer linkers to the solid support, followed by photochemical coupling of the nucleic probes to the microarray. A customizable microarray kit is provided that contains the solid support, linkers, probes, solvent mixture and instructions to use the kit.

Abstract: Provided herein are methods for preparing a sequencing library that includes nucleic acids from a plurality of single cells. In one embodiment, the sequencing library includes whole genome nucleic acids from the plurality of single cells. In one embodiment, the method includes generating nucleosome-depleted nuclei by chemical treatment while maintaining integrity of the nuclei. Also provided herein are compositions, such as compositions that include chemically treated nucleosome-depleted isolated nuclei.