54results about "Library tags" patented technology

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.

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.

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 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 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.

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.

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.

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 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.

Disclosed herein include systems, methods, compositions, and kits for generating protected cellular component-binding compositions. There are provided, in some embodiments, protected cellular component-binding compositions comprising a cellular component-binding reagent associated with a protected cellular component-binding reagent specific oligonucleotide. A protected cellular component-binding reagent specific oligonucleotide can comprise a terminal blocked region. In some embodiments, the 3′ end of the protected cellular component-binding reagent specific oligonucleotide is incapable of being extended by a reverse transcriptase or a polymerase.

Methods of processing multicellular tissue specimens for microscopic imaging for expansion microscopy and processing image datasets obtained therefrom. Cells in the multicellular tissue section are cellularly barcoded using a plurality of epitope tags, wherein the barcoding comprises at least 10, 25, 50, 100, 250, 500, 1000, 2500, 5000, 10000, 25000, or 100,000, or more spectral color combinations, and image datasets are processed using a series of trained neural networks enabling robust segmentation and precise mapping of cellular identity.

A method for characterizing proteins, including steps of (a) detecting a plurality of proteins, wherein individual proteins of the plurality are associated with unique identifiers, wherein the detecting distinguishes the identities of the individual proteins and the unique identifiers associated with the individual proteins; (b) digesting the proteins to form peptides, wherein the peptides from each protein are associated with the unique identifiers for the respective individual protein; (c) detecting the peptides and associated unique identifiers, wherein the detecting distinguishes characteristics of individual peptides, and wherein the detecting distinguishes unique identifiers associated with the individual peptides; and (d) correlating characteristics detected in step (c) with individual proteins detected in step (a) based on the unique identifiers associated with the individual proteins and the peptides.

Provided herein, among other things, is a method for spatial single cell analysis. In some embodiments, the method may comprise: obtaining a cellular sample comprising nucleic acid molecules, binding spatial tags to the sample, removing any unbound or unreacted spatial tags, determining the location and identity of the spatial tag, dissociating the sample into single cells, performing single cell sequencing, determine the spatial barcode for each single cell, and assigning the single cell sequencing reads to its spatial location.

The present invention provides methods of generating diverse chemical structures on DNA through Wittig olefination of novel on-DNA phosphorane ylides and Homer-Wadsworth-Emmons reaction of on-DNA β-keto phosphonates. The methods of this invention provide access to DNA-encode libraries (DELs) of diverse peptides, peptidomimetics, chalcone-based molecules, and the like.

Provided herein are methods of differentiating cells in a cell population that includes detecting fluorescent signals emitted by at least one set of fluorescent barcoding proteins in the cell population to produce a first detected fluorescent signal data set, in which a first subset of the cells in the cell population each comprise a first fluorescent barcoding protein that comprises at least one copy of a first fluorescent protein (FP), or a functional portion thereof, and at least one copy of a second FP, or a functional portion thereof, and in which the first and second FPs, or the functional portions thereof, differ from one another. The methods also include identifying the first fluorescent barcoding protein in the first subset of the cells in the cell population using the first detected fluorescent signal data set. Related methods, compositions, kits, systems, and computer readable media are also provided.

The disclosure relates to compositions and systems comprising nucleic acid sequences that encode and amino acid sequences that comprise a first, second, and third region, each region forming a confirmational trimer and scaffold to associate with and identify certain epitopes against which Immunotherapeutics may bind. Methods of using the polypeptide sequences are also disclosed.

The present invention is concerned with compositions and methods for improving the rate of correct sample identification in indexed nucleic acid library preparations for multiplex next generation sequencing by blocking the 3′ ends of pooled indexed polynucleotides from multiple samples prior to amplification and sequencing, by exonuclease treatment and optionally blocking the 3′ ends of pooled indexed polynucleotides from multiple samples prior to amplification and sequencing, by exonuclease treatment after protective adapters are ligated to target polynucleotides to degrade unincorporated adapters prior to amplification and sequencing, and / or by modifying or blocking 5′ and 3′ ends of pooled indexed polynucleotides from multiple samples, with an optional exonuclease treatment, prior to amplification and sequencing.

Provided is a polypeptide-encoded nucleic acid or small molecule compound library. The library comprises polypeptide barcode tags and nucleic acid molecules or small molecule compounds corresponding to the polypeptide barcode tags. Further provided is a polypeptide-encoded nucleic acid or small molecule compound library, the library comprising a plurality of beads, and each bead comprising a polypeptide barcode tag connected to the bead and a nucleic acid molecule or a small molecule compound corresponding to the polypeptide barcode tag. Further provided is a method for screening a target nucleic acid or small molecule via the polypeptide-encoded nucleic acid or small molecule compound library, wherein a screened nucleic acid molecule or small molecule compound is identified by decoding a polypeptide barcode tag associated therewith.

The present disclosure relates to compositions of matter, methods, and systems for analyzing polymeric macromolecules, including polymeric macromolecules such as peptides, polypeptides, and proteins.

A marker for analysing a biological sample includes an affinity reagent comprising an affinity reagent oligonucleotide with a barcode sequence, a label comprising a label oligonucleotide with a complementary barcode sequence at least partially complementary to the barcode sequence of the affinity reagent oligonucleotide, and at least one blocking oligonucleotide with a blocking sequence that is partially complementary to the barcode sequence of the affinity reagent oligonucleotide or to the complementary barcode sequence of the label oligonucleotide.

The present invention relates to system and methods for robust mapping of single guide RNAs (sgRNAs) in plants, the methods enable the association of specific sgRNA sequences with individual plants.

A method for sequencing a polypeptide is provided. In certain embodiments, the method includes: labeling the N-terminal amino acid of the polypeptide with a nucleic acid label comprising a unique molecular identifier and a 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, wherein 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 foregoing steps are performed sequentially to produce a plurality of such extension products, which are then sequenced, allowing the amino acid sequence of the polypeptide to be determined. Compositions and kits for use in carrying out the method are also provided.

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:         β-Loop     αTAMRA- KKITV-X1X2X3X4- KTYTE- GC- NH2 wherein X1, X2, X3 and X4 are independently arbitrary amino acid residues, and the peptides are immobilized on a chip.

The present invention relates generally to genomics. Some embodiments are directed to imaging the 3D organization of a genome or a portion of a genome in sequence space with high throughput. Some embodiments are directed to imaging the 3D organization of a genome or a portion of a genome with respect to transcriptional activity and nuclear structure. In addition, certain embodiments are directed to chromatin structure, 3D chromatin organization, chromosomal trans-interactions, and chromatin-nuclear structure interactions, and their relationship to transcription. In addition, various embodiments are directed to imaging methods that enable mapping of the 3D organization of a genome or a portion of a genome with respect to nuclear structure and transcriptional activity. Some embodiments are directed to massively multiplexed fluorescence in situ hybridization methods for imaging chromatin loci and / or nascent RNA transcripts at the chromosomal or genome scale.

In a first aspect, a marker (100, 200) for analyzing a biological sample is provided. The marker (100, 200) comprises an affinity reagent (104) comprising an affinity reagent oligonucleotide (108) having a barcode sequence (110). The marker (100, 200) further comprises a marker (112) comprising a marker oligonucleotide (114) having a complementary barcode sequence (116) that is at least partially complementary to the barcode sequence (110) of the affinity reagent oligonucleotide (108). The marker (100, 200) further comprises at least one blocking oligonucleotide (102, 202) having a blocking sequence (118, 204) that is only partially complementary to the barcode sequence (110) of the affinity reagent oligonucleotide (108) or to the complementary barcode sequence (116) of the marker oligonucleotide (114).