175results about "Library tags" patented technology

The present disclosure relates to methods for high-throughput analysis of proteins and peptides employing a set of engineered binders that recognize terminal amino acid residues of peptide analytes. In particular, disclosed herein is the analysis of occupancy of N-linked glycosylation sites in proteins and peptides. The disclosure finds utility at large-scale profiling of N-linked glycosylation sites, as well as monitoring changes in glycosylation patterns associated with numerous disease conditions.

Compositions, methods and systems for targeted delivery using one or more shuttles operably linked to one or more cargos (e.g., cargo polypeptides, e.g., cargo oligonucleotides) and subsequent quantification of an abundance of one or more cargos (e.g, proteins) in a mixture (e.g., a complex mixture (e.g., in vivo)) or in a specific cell, tissue, or organ of interest (e.g., in vivo) using barcodes (e.g., peptide barcodes), binders (e.g., polypeptide binders), and binding agents (e.g., phage) are provided herein.

Kits and methods of analyzing macromolecules, including peptides, polypeptides, and proteins, using nucleic acid coding are disclosed. Sample analysis kits employ nucleic acid coding and / or nucleic acid recording of molecular interactions and / or reactions, such as recognition events (e.g., between antigens and antibodies, between modified terminal amino acid residues, or between small molecules or peptide therapeutic agents and targets, etc. Additional barcoding reagents, such as reagents for cycle-specific barcoding (e.g., "timing"), compartment barcoding reagents, combined barcoding reagents, spatial barcoding reagents, or any combination thereof, may be included in the kit. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may produce molecular interaction and / or reaction information, and / or polypeptide sequence information. The kits can be used for high throughput, multiplexing and / or automated analysis, and are suitable for the analysis of proteomes or subsets thereof.

A method for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding is disclosed.

The invention generally relates to performing sandwich assays in droplets. In certain embodiments, the invention provides methods for detecting a target analyte that involve forming a compartmentalized portion of fluid including a portion of a sample suspected of containing a target analyte and a sample identifier, a first binding agent having a target identifier, and a second binding agent specific to the target analyte under conditions that produce a complex of the first and second binding agents with the target analyte, separating the complexes, and detecting the complexes, thereby detecting the target analyte.

Kits and methods of using the kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and / or nucleic acid recording of a molecular interaction and / or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Additional barcoding reagents, such as those for cycle-specific barcoding (e.g., “clocking”), compartment barcoding, combinatorial barcoding, spatial barcoding, or any combination thereof, may be included in the kits. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may generate molecular interaction and / or reaction information, and / or polypeptide sequence information. The kits may be used in high-throughput, multiplexed, and / or automated analysis, and are suitable for analysis of a proteome or subset thereof.

A method for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding is disclosed.

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

Kits and methods of using the kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and / or nucleic acid recording of a molecular interaction and / or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Additional barcoding reagents, such as those for cycle-specific barcoding (e.g., “clocking”), compartment barcoding, combinatorial barcoding, spatial barcoding, or any combination thereof, may be included in the kits. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may generate molecular interaction and / or reaction information, and / or polypeptide sequence information. The kits may be used in high-throughput, multiplexed, and / or automated analysis, and are suitable for analysis of a proteome or subset thereof.

The invention provides a large-scale imprinting method for copying a template microchip.

Methods, systems, and devices are provided for identification and selective amplification of a correctly assembled nucleic acid comprising a sequence of interest from a mixture of assembled nucleic acids. In some aspects, the inventions use split-pool enzymatic DNA synthesis to add a bead-specific index sequence to bead-bound clonally amplified assembled nucleic acids. High-throughput sequencing is used to identify beads comprising correctly assembled, sequence-perfect nucleic acids. A correctly assembled nucleic acid may be selectively amplified using a primer comprising a sequence that is complementary to the bead-specific index sequence that is associated with the correctly assembled nucleic acid.

Kits and methods of using the kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and / or nucleic acid recording of a molecular interaction and / or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Additional barcoding reagents, such as those for cycle-specific barcoding (e.g., "clocking"), compartment barcoding, combinatorial barcoding, spatial barcoding, or any combination thereof, may be included in the kits. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may generate molecular interaction and / or reaction information, and / or polypeptide sequence information. The kits may be used in high-throughput, multiplexed, and / or automated analysis, and are suitable for analysis of a proteome or subset thereof.

Provided herein are compositions and methods for normalizing sequencing libraries. Further provided herein are adapter conjugates and hybrid circular adapters, composition comprising the same, and methods of generating the same. Further provided herein are methods of using the adapter conjugates, hybrid circular adapters, and compositions comprising the same to normalize genomic DNA libraries for next-generation sequencing.

The present disclosure belongs to the field of molecular biology, particularly to the technical field of gene analysis and detection, and specifically relates to a method for preparing a DNA library and a method for detecting a retroviral integration site. Specifically, the method for preparing the DNA library comprises the following steps: 1) fragmenting a genomic DNA from a retrovirus-infected cell to obtain DNA fragments; 2) subjecting the DNA fragments to end-repair, A-tailing, and ligation with an adapter to obtain a ligation product, wherein the adapter is an asymmetric double-strand adapter comprising a long-strand sequence and a short-strand sequence, wherein the long-strand sequence sequentially comprises, from a 5' end to a 3' end, a fixed sequence, a random UMI sequence, and an amplification primer binding sequence, and the short-strand sequence comprises a sequence complementary to the fixed sequence; and other steps. The detection method of the present disclosure has extremely high sensitivity, thus having good application potential.

The present disclosure relates to methods and kits for analyzing a macromolecule. In some embodiments, the present disclosure relates to macromolecule analysis methods which employ barcoding and nucleic acid encoding of molecular recognition events. Also provided herein is a method and related kits for transferring information using a plurality of enzymes, including for performing a ligation, extension, and cleavage reaction with nucleic acid molecules associated with the macromolecule for analysis. In some embodiments, the macromolecule for analysis comprises a peptide, a polypeptide, or a protein.

In an aspect, a method for evaluating the partitioning of nucleic acid molecules in a sample of polynucleotides based on epigenetic state, comprising: (a) adding a set of epigenetic-control nucleic acid molecules to the nucleic acid molecules in the sample of polynucleotides, whereby producing a spiked-in sample; (b) partitioning nucleic acid molecules of the spiked-in sample into plurality of partitioned sets; (c) enriching a subset of molecules from the plurality of partitioned sets to generate enriched molecules, wherein the enriched molecules comprises a group of epigenetic-control nucleic acid molecules and a group of nucleic acid molecules from the sample of polynucleotides; (d) sequencing the enriched molecules to produce sequencing reads; (e) analyzing the sequencing reads to generate one or more epigenetic partition scores of the epigenetic-control nucleic acid molecules; and (f) comparing the one or more epigenetic partition scores with one or more epigenetic partition cutoffs.

Micron scale biogeography is a major driver of physiology and ecology of complex microbial biofilm communities, which remains elusive largely due to the lack of tools for spatially resolved phylogenetic mapping. This disclosure provides methods, computer-readable storage devices and kits that allow highly multiplexed and spatially resolved imaging of microbial community spatial organization. The disclosure provides a highly-multiplexed approach to resolve the spatial structure of complex microbial community at high taxonomic resolution.

Embodiments of a method and / or system can include generating a set of quality control template (QCT) molecules; determining a set of QCT sequence read clusters based on the set of QCT molecules, such as based on variation regions of the set of QCT molecules; and based on the set of QCT sequence read clusters, determining a sequencing-related parameter, such as a contamination parameter and / or molecule count parameter, associated with the at least one of sequencing library preparation and sequencing.

The present invention provides a method for constructing a cyclic compound library that overcomes the limitations of conventional ring-closing methods for cyclic compound libraries, has the advantages of milder ring-closing reaction conditions and high generality, can be used to construct monocyclic and bicyclic compound libraries, and involves few side reactions. [Solution] A cyclic compound library and its construction method are provided, which uses a solid support, a molecule containing a photocleavable group, a linker, a building block, a ring-closing A-terminal molecule, and a ring-closing B-terminal molecule at both ends of the reaction synthesis, and utilizes the decomposition of the solid support under light irradiation to complete ring closure of the amino acid residue structures of the ring-closing A-terminal molecule A and the ring-closing B-terminal molecule B through the action of cyclohydrolase. This method, which uses mild ring closure conditions, is more universal and expands the types of chemical reactions and the diversity of the encoded compound library.

The present disclosure provides, among other things, a way to amplify and sequence target sequences in a low-input sample. In some embodiments, the method comprises ligating a double-stranded adaptor onto a population of fragments to produce tagged fragments, and linearly amplifying the tagged fragments.

Embodiments of a method and / or system can include generating a set of quality control template (QCT) molecules; determining a set of QCT sequence read clusters based on the set of QCT molecules, such as based on variation regions of the set of QCT molecules; and based on the set of QCT sequence read clusters, determining a sequencing-related parameter, such as a contamination parameter and / or molecule count parameter, associated with the at least one of sequencing library preparation and sequencing.

The present disclosure provides methods and compositions for preparing DNA molecules useful for determining the methylation status of selected regions of a DNA molecule, which utilize methylation-sensitive restriction enzymes and typically involve the amplification or selective enrichment of one or more target regions.

The present disclosure relates to compositions, methods, and systems for analyzing polymeric macromolecules, including polymeric macromolecules such as peptides, polypeptides, and proteins. The methods and compositions described herein can be useful for determining the identity and positional information of amino acid residues of peptides. A peptide can be coupled to a solid support, the N-terminal amino acid of the peptide can be cleaved, and the N-terminal amino acid can be contacted with a chemically reactive conjugate that couples the N-terminal amino acid to the solid support with a cycle tag.

The present application provides a method of producing a “liquid” array of ligand (such as glycan) modified bacteriophage where the ligand modification is encoded genetically within the bacteriophage genome. This method will allow for the determination of the ligand binding profile of biomacromolecules and cells. Furthermore the method allows the elucidation of ligand-protein interactions where ligand binding is co-operative and synergistic.

Provided herein, among other things, is method for analyzing a sample. In some embodiments, the method may comprise: contacting a planar biological sample with an exogenous oligonucleotide or a conjugate comprising antibody and oligonucleotide under conditions by which the exogenous oligonucleotide or conjugate specifically binds to sites in or on the sample, performing one or more steps to cleave and / or extend, e.g. by primer extension or ligation, the exogenous oligonucleotide or complement thereof in situ, placing the sample in contact with a planar support; and incubating the sample and planar support at an elevated temperature, thereby transferring the products to the planar support in a way that preserves the spatial relationship of the products in the sample.

Disclosed herein include systems, methods, compositions, and kits for prevention of antibody oligonucleotide extension. There are provided, in some embodiments, blocking oligonucleotides. In some embodiments, the blocking oligonucleotide comprises a binding region capable of hybridizing barcoding oligonucleotides to form a protected duplex. The blocking oligonucleotide can be a locked nucleic acid (LNA), a peptide nucleic acid (PNA), a DNA, an LNA / PNA chimera, an LNA / DNA chimera, or a PNA / DNA chimera. In some embodiments, the 3′ end of a blocking oligonucleotide is incapable of being extended by a reverse transcriptase or a polymerase. In some embodiments, the blocking oligonucleotide of a protected duplex is incapable of being removed by the strand displacement activity of a reverse transcriptase or a polymerase.