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公开(公告)号:US20240376521A1
公开(公告)日:2024-11-14
申请号:US18661391
申请日:2024-05-10
Applicant: 10x Genomics, Inc.
Inventor: Justin COSTA , Cheyenne CHRISTOPHERSON
IPC: C12Q1/6806 , C12N9/12 , C12N9/22 , C12Q1/6876
Abstract: The present disclosure relates in some aspects to methods and boronic acid compositions for immobilizing RNA analytes in biological samples, and more specifically fragmented RNAs. RNA analytes may be tethered covalently or non-covalently to exogenous or endogenous molecules in a biological sample, for example, cross-linked directly to a polymerized three-dimensional matrix.
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公开(公告)号:US20240175082A1
公开(公告)日:2024-05-30
申请号:US18488502
申请日:2023-10-17
Applicant: 10x Genomics, Inc.
Inventor: Justin COSTA
IPC: C12Q1/6841 , C12Q1/682
CPC classification number: C12Q1/6841 , C12Q1/682
Abstract: The present disclosure in some aspects relates to methods and compositions for analyzing a biological sample comprising contacting the biological sample with a molecule comprising a branched linker. In some embodiments, the molecule is a detectable probe comprising branches each comprising one or more detectable labels and/or one or more sequences for hybridizing to a detectably labeled probe. In some embodiments, the molecule comprises an oligonucleotide linked to photoactivatable functional moieties via a branched linker.
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公开(公告)号:US20240351041A1
公开(公告)日:2024-10-24
申请号:US18634751
申请日:2024-04-12
Applicant: 10x Genomics, Inc.
Inventor: Cheyenne CHRISTOPHERSON , Justin COSTA , Shalini GOHIL , Hong CHEN , Yufeng QIAN , Minkyung PARK , Xiaoyang CAI , Hiroshi SASAKI , Naveed BAKH
IPC: B01L3/00
CPC classification number: B01L3/527 , B01L2200/025 , B01L2200/0689 , B01L2200/16 , B01L2300/044 , B01L2300/12
Abstract: The present disclosure provides systems and methods for reagent storage. System may include one or more substrates comprising a partition. The partition may be configured to retain a first reagent separate from a second reagent. The partition may include a seal disposed between the first and second reagent. The seal may be configured to maintain the first reagent separate from the second reagent. The first and second reagent may be disposed in a first layer and a second layer, respectively, of frozen material. The first layer and second layer of frozen material may maintain the first reagent separate from the second reagent.
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公开(公告)号:US20230242974A1
公开(公告)日:2023-08-03
申请号:US18088330
申请日:2022-12-23
Applicant: 10x Genomics, Inc.
Inventor: Justin COSTA , Jorge Iván HERNÁNDEZ NEUTA
IPC: C12Q1/6841 , C12Q1/6855
CPC classification number: C12Q1/6841 , C12Q1/6855
Abstract: The present disclosure in some aspects relates to methods and compositions for detecting and quantifying multiple analytes present in a biological sample by rolling circle amplification (RCA). In some aspects, the methods and compositions provided herein address issues associated with control of signal spot size and intensity for RCA products (RCPs) in a sample. In some aspects, provided herein are methods and compositions (e.g., probes and/or reaction mixtures) for slowing down RCA and/or decreasing the size of RCA products. In some embodiments, nucleotides or nucleotide analogs having a hydrophobic group (e.g., a hydrophobic modification on the base) are included in nucleotides for RCA and incorporated into the RCP product, leading to reduction of RCP size without the need of crosslinking an incorporated hydrophobic nucleotide or nucleotide analog to the RCP itself or another molecule.
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公开(公告)号:US20230159997A1
公开(公告)日:2023-05-25
申请号:US17993793
申请日:2022-11-23
Applicant: 10x Genomics, Inc.
Inventor: Zahra Kamila BELHOCINE , Justin COSTA , Eswar Prasad RAMACHANDRAN IYER
IPC: C12Q1/6841 , C12Q1/682 , C12Q1/6844
CPC classification number: C12Q1/6841 , C12Q1/682 , C12Q1/6844
Abstract: The present disclosure relates in some aspects to methods and compositions for analyzing a target nucleic acid, such as in situ detection of a region of interest in a polynucleotide in a cell or tissue sample. In some aspects, provided herein are circular probes (e.g., dumbbell probes) for analyzing a target nucleic acid, as well as methods comprising an enzymatic treatment to de-circularize unbound or non-specifically bound circular probes. Circular probes specifically bound to target nucleic acids remain intact during and after the enzymatic treatment and can be detected, e.g., via rolling circle amplification (RCA) of the circular probes and detection of the RCA products.
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公开(公告)号:US20240218424A1
公开(公告)日:2024-07-04
申请号:US18391284
申请日:2023-12-20
Applicant: 10x Genomics, Inc.
Inventor: Justin COSTA , Meiliana TJANDRA
IPC: C12Q1/6806 , C12Q1/37 , C12Q1/48 , C12Q1/6844
CPC classification number: C12Q1/6806 , C12Q1/37 , C12Q1/485 , C12Q1/6844
Abstract: The present disclosure relates in some aspects to methods and compositions for immobilizing ribonucleic acid analytes in biological samples, and more specifically fragmented ribonucleic acids. Ribonucleic acid analytes may be tethered covalently or non-covalently to exogenous or endogenous molecules in a biological sample, for example, cross-linked directly to a polymerized three-dimensional matrix.
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公开(公告)号:US20240167081A1
公开(公告)日:2024-05-23
申请号:US18503949
申请日:2023-11-07
Applicant: 10x Genomics,Inc.
Inventor: Felice Alessio BAVA , Cheyenne CHRISTOPHERSON , Justin COSTA , Shalini GOHIL , Christina GALONSKA , Monica NAGENDRAN
IPC: C12Q1/682 , C12Q1/6841 , C12Q1/6844 , C12Q1/6876 , G01N1/30
CPC classification number: C12Q1/682 , C12Q1/6841 , C12Q1/6844 , C12Q1/6876 , G01N1/30
Abstract: The present disclosure relates in some aspects to methods and compositions for immobilization of nucleic acids for in situ detection in a biological sample or a matrix embedding the biological sample.
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公开(公告)号:US20240026448A1
公开(公告)日:2024-01-25
申请号:US18204264
申请日:2023-05-31
Applicant: 10x Genomics, Inc.
Inventor: Justin COSTA
IPC: C12Q1/6876 , C12Q1/6813 , G01N21/35
CPC classification number: C12Q1/6876 , C12Q1/6813 , G01N21/35 , C12Q2600/16
Abstract: The present disclosure relates in some aspects to methods and compositions for in situ analysis using nucleic acid complexes comprising a detectable label and a moiety that can be activated to extinguish signals of the detectable label. In some embodiments, the activatable moiety comprises a photosensitizer. The nucleic acid complexes may allow for improved detection and decreased signal carryover between detection cycles.
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公开(公告)号:US20230057571A1
公开(公告)日:2023-02-23
申请号:US17816995
申请日:2022-08-02
Applicant: 10x Genomics, Inc.
Inventor: Justin COSTA , Jorge Iván HERNÁNDEZ NEUTA , Patrick J. MARKS
IPC: C12Q1/6837 , C12Q1/6816 , C12Q1/682 , C12Q1/6832 , C12Q1/6841 , C12Q1/6844 , C12Q1/6876
Abstract: The present disclosure in some aspects relates to methods and compositions for accurately detecting and quantifying multiple analytes present in a biological sample. In some aspects, the methods and compositions provided herein address one or more issues associated with the stability and/or size of nucleic acid structures, such as RCPs, in the biological sample without the use of exogenously added oligonucleotide compaction probes. In some embodiments, provided herein are methods involving the use of self-hybridizing hybridizing regions for compacting and/or stabilizing nucleic acid concatemers (e.g., RCPs). In some embodiments, dynamic inter-strand annealing between tandem units of an RCP is used for compaction and/or stabilization. In some embodiments, short palindromic regions in an RCP are used for compaction and/or stabilization.
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公开(公告)号:US20250163502A1
公开(公告)日:2025-05-22
申请号:US18955449
申请日:2024-11-21
Applicant: 10x Genomics, Inc.
Inventor: Justin COSTA , Yina LI , Meiliana TJANDRA
IPC: C12Q1/6841
Abstract: The present disclosure relates in some aspects to methods and compositions for repairing and/or immobilizing ribonucleic acid analytes in biological samples, and more specifically fragmented ribonucleic acids. A workflow is provided for polishing and repairing fragmented ribonucleic acids in a biological sample, for improving nucleic acid quality for downstream applications, such as in situ, spatial array, or single-cell based analysis. Ribonucleic acid analytes may be tethered covalently or non-covalently to a matrix-forming agent, for example, matrix-forming agent that can form a three-dimensional polymerized matrix.
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