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    METHODS FOR BARCODING MACROMOLECULES IN INDIVIDUAL CELLS
    3.
    发明公开
    METHODS FOR BARCODING MACROMOLECULES IN INDIVIDUAL CELLS 审中-公开

    公开(公告)号：US20230332215A1

    公开(公告)日：2023-10-19

    申请号：US18322490

    申请日：2023-05-23

    申请人： Encodia, Inc.

    发明人： Mark S. CHEE ,  Haibiao GONG ,  Kevin L. GUNDERSON

    IPC分类号： C12Q1/6841

    CPC分类号： C12Q1/6841 ,  C12Q1/6806

    摘要： The present disclosure relates to methods and kits for generating single cell barcodes and imparting them to the constituent molecules within a single cell. Additionally, methods to overlay sample barcode and spatial barcode information onto the single cell barcodes are also described. Generation of single cell barcodes is achieved by labeling the genomic DNA of a cell/nucleus with a small handful, preferably just a one or two cellular barcode probes (CBP) that can be amplified and propagated to label the constituent molecules within the cell. The disclosure finds utility in applications such as characterization of cellular heterogeneity, comprehensive profiling of tissue composition, characterization of adherent cells, discovery of new cell subtypes and functions of individual cells in the context of its microenvironment, and others.

    Methods for preparing analytes and related kits
    5.
    发明授权
    Methods for preparing analytes and related kits 有权

    公开(公告)号：US11634709B2

    公开(公告)日：2023-04-25

    申请号：US17458199

    申请日：2021-08-26

    申请人： Encodia, Inc.

    发明人： Mark S. Chee ,  Kevin L. Gunderson ,  Norihito Muranaka ,  Brian Tate Weinert

    IPC分类号： C12N15/10

    摘要： Provided herein are methods for preparing and treating an analyte (e.g., a macromolecule or a plurality of macromolecules, peptides, polypeptides, and proteins) for analysis. In some embodiments, the analyte is prepared and treated in a method that includes the use of bait and capture nucleic acids, solid supports, and reaction mixtures including the bait and capture nucleic acids. In some embodiments, the analyte is coupled to a solid support. Also provided are kits containing components for performing the provided methods for preparing the analytes. In some embodiments, the methods are for preparing an analyte for sequencing. Provided herein are methods for preparing and treating an analyte (e.g., a macromolecule or a plurality of macromolecules, peptides, polypeptides, and proteins) for analysis. In some embodiments, the analyte is prepared and treated in a method that includes the use of bait and capture nucleic acids, solid supports, and reaction mixtures including the bait and capture nucleic acids. In some embodiments, the analyte is coupled to a solid support. Also provided are kits containing components for performing the provided methods for preparing the analytes. In some embodiments, the methods are for preparing an analyte for sequencing.

    METHODS OF POLYPEPTIDE SEQUENCING
    6.
    发明申请
    METHODS OF POLYPEPTIDE SEQUENCING 有权

    公开(公告)号：US20230016396A1

    公开(公告)日：2023-01-19

    申请号：US17848010

    申请日：2022-06-23

    申请人： ENCODIA, INC.

    发明人： Kevin L. GUNDERSON ,  Norihito MURANAKA ,  Lei SHI ,  Stephen VERESPY, III

    IPC分类号： G01N33/68 ,  G01N33/58 ,  C12N9/48

    摘要： The present disclosure relates to methods and kits for performing an identification of a terminal amino acid residue of the polypeptide, or performing a polypeptide sequencing. The methods include a step of contacting the terminal amino acid residue of the polypeptide with a coupler, followed by attaching the coupler-polypeptide complex to the solid support and cleaving the coupler-polypeptide complex from the polypeptide, thereby isolating the terminal amino acid residue of the polypeptide from the remaining amino acid residues of the polypeptide in complex with the coupler, thereby enabling efficient identification of the terminal amino acid residue via recognition by binding agents capable of binding to the coupler-amino acid complex. In some embodiments, the coupler and the polypeptide are both associated with stabilizing components, and after binding of the coupler to the terminal amino acid of the polypeptide, tethering complex is formed between the stabilizing components releasably attached to the solid support.

    METHODS FOR STABLE COMPLEX FORMATION AND RELATED KITS
    8.
    发明申请
    METHODS FOR STABLE COMPLEX FORMATION AND RELATED KITS 有权

    公开(公告)号：US20220214350A1

    公开(公告)日：2022-07-07

    申请号：US17505557

    申请日：2021-10-19

    申请人： Encodia, Inc.

    发明人： Kevin L. GUNDERSON ,  Norihito MURANAKA

    IPC分类号： G01N33/58 ,  G01N33/68 ,  G01N33/53

    摘要： The present disclosure relates to methods and kits for forming a stable complex comprising a binding agent and a target (e.g., a macromolecule). In some embodiments, the target comprises a peptide, a polypeptide, or a protein to be analyzed. In some embodiments, the present disclosure relates to formation of a stable complex comprising a binding agent and a target (e.g., a macromolecule) to be analyzed in a method which employs barcoding and nucleic acid encoding of molecular recognition events, and/or detectable labels. Provided herein is also a programmable system for information transfer comprising one or more adaptor molecules.

    POLYPEPTIDE MODIFICATION AND CONJUGATION METHODS
    10.
    发明公开
    POLYPEPTIDE MODIFICATION AND CONJUGATION METHODS 审中-公开

    公开(公告)号：US20240000947A1

    公开(公告)日：2024-01-04

    申请号：US18201129

    申请日：2023-05-23

    申请人： Encodia, Inc.

    发明人： Stephen VERESPY, III ,  Samantha BEASLEY

    IPC分类号： A61K47/54

    CPC分类号： A61K47/542 ,  A61K47/547

    摘要： The present disclosure relates to a selective and efficient method to connect a polypeptide containing at least one lysine residue to a cargo moiety, where one step of the method involves reaction of a semicarbazide group with an ortho-acylphenyl boronic acid, forming a cyclic diazaborine ring fused to phenyl. Conditions for formation of the cyclic diazaborine are sufficiently mild for the method to be used in the presence of sensitive biomolecules such as polynucleotides. A substituent group on the phenyl can be used to link the cyclic diazaborine to a cargo moiety such as a polynucleotide, bead, or reactive group, providing a polypeptide—cargo moiety conjugate that is useful for various purposes, such as to analyze, identify, track, locate, detect, or immobilize the polypeptide. Also provided are polypeptide—cargo moiety conjugates, wherein the polypeptide and cargo moiety are connected via a linker that comprises a cyclic diazaborine.