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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.
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.
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公开(公告)号：US20230279386A1
公开(公告)日：2023-09-07
申请号：US18190001
申请日：2023-03-24
申请人： Encodia, Inc.
IPC分类号： C12N15/10
CPC分类号： C12N15/1065
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.
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公开(公告)号：US12130291B2
公开(公告)日：2024-10-29
申请号：US17819263
申请日：2022-08-11
申请人： Encodia, Inc.
发明人： Mark S. Chee , John M. Beierle , Norihito Muranaka , Kevin L. Gunderson , Michael Phillip Weiner , Lei Shi , Robert C. James , Luca Monfregola
CPC分类号： G01N33/6842 , C40B40/10 , C40B70/00 , G01N33/6845
摘要： 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.
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公开(公告)号：US20240294965A1
公开(公告)日：2024-09-05
申请号：US18658862
申请日：2024-05-08
申请人： Encodia, Inc.
发明人： Eric OKERBERG , Kevin L. Gunderson , Norihito Muranaka , Jongbum Kim , Byung Joon Lim , Lei Shi , Soumya Ganguly , Devin Sullivan
IPC分类号： C12Q1/6804 , G01N33/569
CPC分类号： C12Q1/6804 , G01N33/56983 , G01N2333/165 , G01N2458/10 , G01N2469/20
摘要： Provided herein are high-throughput, population-wide serotyping and antibody profiling assays. Disclosed variants of a Digital Serotyping assay employ next generation sequencing to measure the “serotyping profile” of barcoded subject serum antibodies tested against a range of DNA-tagged pathogen-derived antigens. The disclosed assay setup enables multiplexing in both the sample and antigen dimensions, generating a large multi-dimensional serotyping data set for more comprehensive serotyping profiling of large populations across a large number of antigens and possible pathogens. Moreover, the ability to easily scale and multiplex the number of peptide epitopes allows rapid updating of the assay content to monitor the ever-changing spectrum of pathogens. Additional applications of this technology include cancer immunology and autoimmune conditions (e.g., neoantigen or autoimmune profiling), screening for toxins, antibody therapeutics development, biosecurity, and veterinary medicine.
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公开(公告)号：US11782062B2
公开(公告)日：2023-10-10
申请号：US18166461
申请日：2023-02-08
申请人： Encodia, Inc.
发明人： Mark S. Chee , John M. Beierle , Norihito Muranaka , Kevin L. Gunderson , Michael Phillip Weiner , Lei Shi , Robert C. James , Luca Monfregola
CPC分类号： G01N33/6842 , C40B40/10 , C40B70/00 , G01N33/6845
摘要： 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.
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公开(公告)号：US11513126B2
公开(公告)日：2022-11-29
申请号：US16760028
申请日：2018-10-31
申请人： Encodia, Inc.
发明人： Mark S. Chee , John M. Beierle , Norihito Muranaka , Kevin L. Gunderson , Michael Phillip Weiner , Lei Shi , Robert C. James , Luca Monfregola
IPC分类号： C12Q1/6804 , G01N33/68 , C40B40/10 , C40B70/00
摘要： 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.
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公开(公告)号：US12129463B2
公开(公告)日：2024-10-29
申请号：US18125075
申请日：2023-03-22
申请人： Encodia, Inc.
IPC分类号： C12N15/10 , C12Q1/6804 , G01N33/68
CPC分类号： C12N15/1065 , C12Q1/6804 , G01N33/68 , G01N2458/10
摘要： Methods and 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.). Assays that do not require the cyclic transfer of information between a coding tag and a recording tag are also disclosed, including single cycle assays.
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公开(公告)号：US12043862B2
公开(公告)日：2024-07-23
申请号：US18089444
申请日：2022-12-27
申请人： Encodia, Inc.
发明人： Eric Okerberg , Kevin L. Gunderson , Norihito Muranaka , Jongbum Kim , Byung Joon Lim , Lei Shi , Soumya Ganguly , Devin Sullivan
IPC分类号： C12Q1/6804 , G01N33/569
CPC分类号： C12Q1/6804 , G01N33/56983 , G01N2333/165 , G01N2458/10 , G01N2469/20
摘要： Provided herein are high-throughput, population-wide serotyping and antibody profiling assays. Disclosed variants of a Digital Serotyping assay employ next generation sequencing to measure the “serotyping profile” of barcoded subject serum antibodies tested against a range of DNA-tagged pathogen-derived antigens. The disclosed assay setup enables multiplexing in both the sample and antigen dimensions, generating a large multi-dimensional serotyping data set for more comprehensive serotyping profiling of large populations across a large number of antigens and possible pathogens. Moreover, the ability to easily scale and multiplex the number of peptide epitopes allows rapid updating of the assay content to monitor the ever-changing spectrum of pathogens. Additional applications of this technology include cancer immunology and autoimmune conditions (e.g., neoantigen or autoimmune profiling), screening for toxins, antibody therapeutics development, biosecurity, and veterinary medicine.
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公开(公告)号：US11169157B2
公开(公告)日：2021-11-09
申请号：US17149324
申请日：2021-01-14
申请人： Encodia, Inc.
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.
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