123results 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.

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

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.

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.

The present invention features a number of methods for identifying one or more compounds that bind to a biological target. The methods include synthesizing a library of compounds, wherein the compounds contain a functional moiety having one or more diversity positions. The functional moiety of the compounds is operatively linked to an initiator oligonucleotide that identifies the structure of the functional moiety.

Provided herein are methods for preparing a sequencing library from a plurality of single cells that includes nucleic acids having three index sequences, as well as methods for generating an RNA sequencing library from single cells that can be used to dissect the critical regulators of gene-specific transcription, splicing, and degradation in a massive-parallel manner. Also provided herein are compositions, such as oligonucleotide sets for generating the sequencing libraries and kits for preparing the sequencing libraries.

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

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.

Peptide sequencing methods are described, in which the non-attached termini of surface end-immobilized peptides are functionalized with a universal docking strand (DS) DNA oligonucleotide. A library of signal molecules (such as fluorophores), each of which is conjugated to an imaging strand (IS) oligo complementary to the DS oligo, is used for characterizing each sequential terminal amino acid of the peptide. Computer assisted analysis is used to identify each amino acid, based on differences in the measured signal that are caused by proximity of the signal molecule(s) to each terminal amino acid.

Disclosed is a fluorescently labeled peptide library useful for diagnosing multiple sclerosis. The fluorescently labeled peptide library comprising fluorescently labeled peptides represented by the following formula:wherein X1, X2, X3 and X4 are independently arbitrary amino acid residues, and the peptides are immobilized on a chip.

Provided are methods of sequencing a polypeptide. In certain embodiments, the methods comprise labeling the N-terminal amino acid of a polypeptide with a nucleic acid label comprising a unique molecular identifier and cycle number barcode; degrading the N-terminal amino acid from the polypeptide; annealing a primer to the nucleic acid label of the degraded amino acid, where the primer comprises a barcode corresponding to the identity of the degraded N-terminal amino acid; and extending the primer annealed to the nucleic acid label to produce an extension product comprising the unique molecular identifier, the cycle number barcode, and the barcode corresponding to the identity of the degraded N-terminal amino acid. The preceding steps are performed successively to produce a plurality of such extension products which are then sequenced, enabling determination of the amino acid sequence of the polypeptide. Composition and kits that find use in practicing the methods are also provided.

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.

The present disclosure relates generally to methods of uniquely labeling or barcoding molecules within immune cells such as B cells, or within nuclei derived therefrom. The present disclosure also relates to kits for uniquely labeling molecules within immune cells such as B cells, or within nuclei derived therefrom. In particular, the methods and kits may relate to the labeling of RNAs and / or cDNA encoding B cell receptors (BCRs) within such cells or nuclei.