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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:US20240327827A1
公开(公告)日:2024-10-03
申请号:US18443854
申请日:2024-02-16
发明人: Eleen Shum
CPC分类号: C12N15/1096 , C12N15/1006 , C40B40/06 , C40B50/04 , C40B50/06 , C40B70/00
摘要: Disclosed herein include systems, methods, compositions, and kits for whole transcriptome analysis (WTA) with random priming and extension (RPE). The RPE-based WTA method can comprise hybridizing random primers with a plurality of first strand barcoded polynucleotides associated with a solid support and extending the random primers to generate a plurality of extension products. The method can comprise amplifying the plurality of extension products to generate a sequencing library.
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公开(公告)号:US12049712B2
公开(公告)日:2024-07-30
申请号:US17229859
申请日:2021-04-13
申请人: 10X Genomics, Inc.
IPC分类号: C40B30/04 , C07K14/74 , C12N15/10 , C12N15/11 , C12N15/85 , C12Q1/6804 , C12Q1/6806 , C12Q1/6818 , C12Q1/6827 , C12Q1/6881 , C40B50/06 , C40B70/00 , G01N33/50 , G01N33/53 , G01N33/532 , G01N33/543 , G01N33/548 , G01N33/569 , G01N33/58
CPC分类号: C40B30/04 , C07K14/70539 , C12N15/1037 , C12N15/1055 , C12N15/1065 , C12N15/1075 , C12N15/11 , C12N15/85 , C12Q1/6804 , C12Q1/6806 , C12Q1/6818 , C12Q1/6827 , C12Q1/6881 , G01N33/5032 , G01N33/505 , G01N33/5304 , G01N33/5306 , G01N33/5308 , G01N33/532 , G01N33/54306 , G01N33/54366 , G01N33/548 , G01N33/56977 , G01N33/58 , C12N2310/20 , C12N2320/10 , C12Q2537/164 , C12Q2563/179 , C12Q2563/185 , C12Q2565/1015 , C40B50/06 , C40B70/00
摘要: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and analyte characterization from a single cell. Such polynucleotide processing may be useful for a variety of applications. The compositions, methods, systems, and devices disclosed herein generally describe barcoded oligonucleotides, which can be bound to a bead, such as a gel bead, useful for characterizing one or more analytes including, for example, protein (e.g., cell surface or intracellular proteins) and chromatin (e.g., accessible chromatin).
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公开(公告)号:US20240175081A1
公开(公告)日:2024-05-30
申请号:US18461672
申请日:2023-09-06
IPC分类号: C12Q1/6841 , C40B30/04 , C40B70/00
CPC分类号: C12Q1/6841 , C40B30/04 , C40B70/00 , C12Q2525/161 , C12Q2563/179 , C12Q2565/514
摘要: The present invention generally relates to imaging cells, for example, to determine phenotypes and/or genotypes in populations of cells. In some aspects, cells may be analyzed, e.g., imaged, to determine their phenotype, and their genotypes may be determined by exposing the cells to nucleic acid probes, e.g., as in smFISH. MERFISH, FISH, in situ hybridization, or other suitable techniques. In some cases, the cells may be exposed to a nucleic acid comprising an identification portion, which may be used to distinguish the cells from each other. In some embodiments, the cells may be exposed to a nucleic acid comprising an expression portion, e.g. a gene, or coding region for a non-translated RNA, etc., that when expressed, produces a protein, RNA, DNA, or the like that may alter the phenotype of the cell or the variable nucleic acid sequence can consist of promoters, gene regulatory elements, transcription factor binding sites, Cas9 guide RNA coding regions, etc. that otherwise alter the phenotype of the cell. In some embodiments, the modifications that contain either the identification portion, the expression portion, or both may be introduced into the genome of a host organism or as exogenous materials, e.g. plasmids. Such changes may involve the addition of synthetic materials, such as synthetic nucleic acids, or modifications, e.g. deletions or mutations, of the genomic material of the host organism. Other aspects are generally directed to compositions or devices for use in such methods, kits for use in such methods, or the like.
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公开(公告)号:US11993773B2
公开(公告)日:2024-05-28
申请号:US17192578
申请日:2021-03-04
申请人: DNA Script SAS
发明人: Xavier Godron , Adrian Horgan , Sylvain Gariel , Jeffrey Jeddeloh , Robert Nicol , Thomas Ybert
CPC分类号: C12N15/1096 , C12N15/111 , C12Q1/44 , C40B50/06 , C40B50/08 , C40B50/14 , C40B70/00 , C12N2310/319 , C12N2310/3515 , C12N2330/31
摘要: The invention is directed to methods for synthesizing oligonucleotides directly on biomolecules or cells living or fixed. In some embodiments, template-free enzymatic synthesis is implemented under biological conditions with successive cycles of (i) enzymatic addition of a 3′-O-blocked nucleoside triphosphate and (ii) enzymatic deblocking of the incorporated nucleotide to regenerate a free 3′ hydroxyl. The invention has applications in single-cell cDNA library construction and analysis.
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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:US11697839B2
公开(公告)日:2023-07-11
申请号:US17068893
申请日:2020-10-13
IPC分类号: C12Q1/6841 , C40B70/00 , C40B40/08 , C12Q1/6816 , C40B20/04
CPC分类号: C12Q1/6841 , C12Q1/6816 , C40B40/08 , C40B70/00 , C40B20/04 , C12Q1/6841 , C12Q2535/00 , C12Q2537/143 , C12Q2563/107 , C12Q2565/514 , C12Q1/6816 , C12Q2535/00 , C12Q2537/143 , C12Q2563/107 , C12Q2565/514
摘要: The present invention relates to a method of identifying a target genomic nucleic acid sequence including hybridizing a set of probes to the target genomic nucleic acid sequence, wherein the set of probes has a unique associated barcode sequence for identification of the target genomic nucleic acid sequence, wherein each probe of the set includes (1) a complementary sequence complementary to a first strand of the target genomic nucleic acid sequence and (2) the associated barcode sequence or a portion of the associated barcode sequence, sequencing the associated barcode sequence from probes hybridized to the target genomic nucleic acid sequence using a fluorescence-based sequencing method, and identifying the target genomic nucleic acid sequence by the sequenced barcode sequence.
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公开(公告)号:US11555185B2
公开(公告)日:2023-01-17
申请号:US16721395
申请日:2019-12-19
发明人: Cynthia Hendrickson , Sarah Bowman , Amy Emerman , Kruti Patel
摘要: 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.
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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:US20220333273A1
公开(公告)日:2022-10-20
申请号:US17728735
申请日:2022-04-25
申请人: Inscripta, Inc.
发明人: Richard Fox , Daniel Held
IPC分类号: C40B50/06 , C12N9/22 , C40B30/04 , C40B40/10 , C07K16/28 , C07K14/74 , C40B70/00 , C12N15/81 , C12N15/85 , C12N15/90 , C40B20/04 , C40B40/02 , C12N15/10
摘要: The present disclosure provides shuttle vectors for editing exogenous polynucleotides in heterologous live cells, as well as automated methods, modules, and multi-module cell editing instruments and systems for performing the editing methods.
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