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    SAMPLE HANDLING APPARATUS AND IMAGE REGISTRATION METHODS
    42.
    发明公开
    SAMPLE HANDLING APPARATUS AND IMAGE REGISTRATION METHODS 审中-公开

    公开(公告)号：US20230351619A1

    公开(公告)日：2023-11-02

    申请号：US18044903

    申请日：2021-09-17

    Applicant: 10x Genomics, Inc.

    Inventor： Augusto Manuel Tentori ,  Hanyoup Kim ,  Siyuan Xing ,  Felice Alessio Bava ,  Rajiv Bharadwaj ,  Cedric Uytingco ,  Erica Graziosa

    IPC: G06T7/33

    CPC classification number: G06T7/33 ,  G01N1/30

    Abstract: A method for aligning a sample to an array is provided. An image of sample image of a sample can be received by a data processor. The sample image having a first resolution. An array image including an overlay of an array with the sample and an array fiducial can be received by the data processor. The array image having a second resolution lower than the first resolution of the sample image. The sample image can be registered to the array image by aligning the sample image and the array image. An aligned image can be generated based on the registering. The aligned image can include an overlay of the sample image with the array. The aligned image can be provided by the data processor. A method for detecting fiducials associated with an array is provided. Systems and non-transitory computer readable mediums performing the method are also provided.

    FLUID DELIVERY METHODS
    44.
    发明申请
    FLUID DELIVERY METHODS 有权

    公开(公告)号：US20230017773A1

    公开(公告)日：2023-01-19

    申请号：US17873586

    申请日：2022-07-26

    Applicant: 10x Genomics, Inc.

    Inventor： Hanyoup Kim ,  Augusto Manuel Tentori ,  Siyuan Xing ,  Rajiv Bharadwaj ,  Bill Kengli Lin ,  Felice Alessio Bava ,  Pratomo Putra Alimsijah ,  Nabil Mikhaiel

    IPC: B01L3/00 ,  C12Q1/6837 ,  G01N1/31 ,  C12Q1/6841

    Abstract: Provided herein is a fluid delivery method for permeabilizing a biological sample. The method includes delivering the fluid to a first substrate and/or a second substrate. At least one of the first substrate and the second substrate includes a spacer. The method further includes assembling, subsequent to the delivering, a chamber comprising the first substrate, the second substrate, the biological sample, and the spacer. The spacer may be disposed between the first substrate and second substrate. The spacer may be configured to maintain the fluid within the chamber and maintain a separation distance between the first substrate and the second substrate. The spacer may be positioned to at least partially surround an area on the first substrate on which the biological sample is disposed and/or at least partially surround the array disposed on the second substrate.

    IMAGING SYSTEM HARDWARE
    45.
    发明申请
    IMAGING SYSTEM HARDWARE 有权

    公开(公告)号：US20220241780A1

    公开(公告)日：2022-08-04

    申请号：US17665169

    申请日：2022-02-04

    Applicant: 10x Genomics, Inc.

    Inventor： Augusto Manuel Tentori ,  Rajiv Bharadwaj ,  Felice Alessio Bava

    IPC: B01L3/00 ,  B01L9/00

    Abstract: A sample holder includes a first member featuring a first retaining mechanism configured to retain a first substrate that includes a sample, a second member featuring a second retaining mechanism configured to retain a second substrate that includes a reagent medium, and an alignment mechanism connected to at least one of the first and second members, and configured to align the first and second members such that the sample contacts at least a portion of the reagent medium when the first and second members are aligned.

    Sample handling apparatus and image registration methods
    46.
    发明授权
    Sample handling apparatus and image registration methods 有权

    公开(公告)号：US12249085B2

    公开(公告)日：2025-03-11

    申请号：US18185599

    申请日：2023-03-17

    Applicant: 10x Genomics, Inc.

    Inventor： Augusto Manuel Tentori ,  Hanyoup Kim ,  Siyuan Xing ,  Felice Alessio Bava ,  Rajiv Bharadwaj ,  Cedric Uytingco ,  Erica Graziosa

    IPC: G06V10/24 ,  G06T7/33 ,  G06V10/25 ,  G01N1/30

    Abstract: A method for aligning a sample to an array is provided. An image of sample image of a sample can be received by a data processor. The sample image having a first resolution. An array image including an overlay of an array with the sample and an array fiducial can be received by the data processor. The array image having a second resolution lower than the first resolution of the sample image. The sample image can be registered to the array image by aligning the sample image and the array image. An aligned image can be generated based on the registering. The aligned image can include an overlay of the sample image with the array. The aligned image can be provided by the data processor. A method for detecting fiducials associated with an array is provided. Systems and non-transitory computer readable mediums performing the method are also provided.

    Nucleic acid assays using click chemistry bioconjugation
    47.
    发明授权
    Nucleic acid assays using click chemistry bioconjugation 有权

    公开(公告)号：US12209273B2

    公开(公告)日：2025-01-28

    申请号：US17346077

    申请日：2021-06-11

    Applicant: 10x Genomics, Inc.

    Inventor： Felice Alessio Bava ,  David M. Patterson ,  Meiliana Tjandra ,  Yi Luo

    IPC: C12Q1/6816

    Abstract: Provided herein are methods of sequencing comprising click chemistry bioconjugation. In some embodiments, target polynucleotide sequences on the same or different molecules are contacted with and hybridize to probes comprising click functional groups. Probes (e.g., reading probes) hybridizing to adaptor sequences adjacent to different sequences of interest (e.g., barcodes to be sequenced) can be hybridized simultaneously in large pools. In some embodiments, the provided methods achieve multiplexing without requiring separate hybridization of probes (e.g., reading probes) for each sequencing-by-ligation cycle, thereby reducing total hybridization time which is typically a most time-consuming step in in situ technologies. In some aspects, the hybridized probes (e.g., reading probes) are clicked onto detectable probes to analyze a sequence of a target polynucleotide in a sequencing-by-ligation fashion.

    Methods and compositions for integrated in situ spatial assay
    49.
    发明授权
    Methods and compositions for integrated in situ spatial assay 有权

    公开(公告)号：US12173360B2

    公开(公告)日：2024-12-24

    申请号：US17180325

    申请日：2021-02-19

    Applicant: 10x Genomics, Inc.

    Inventor： Felice Alessio Bava ,  Zachary Bent

    IPC: C12Q1/68 ,  C12Q1/6837 ,  C12Q1/6844

    Abstract: In some embodiments, provided herein is an integrated assay of a biological sample comprising an in situ assay module and a spatial assay module. The in situ assay comprises analyzing binding between nucleic acid probes and a first analyte at a spatial location of the biological sample. In some embodiments, the method further comprises providing conditions to allow spatially barcoded capture agents to capture a second analyte for analysis in the spatial assay module.

    Methods for preparing high-resolution spatial arrays
    50.
    发明授权
    Methods for preparing high-resolution spatial arrays 有权

    公开(公告)号：US12110541B2

    公开(公告)日：2024-10-08

    申请号：US17165453

    申请日：2021-02-02

    Applicant: 10x Genomics, Inc.

    Inventor： Felice Alessio Bava

    IPC: C12Q1/6837 ,  C12Q1/6874

    CPC classification number: C12Q1/6837 ,  C12Q1/6874

    Abstract: Provided herein are methods of preparing a spatial array and methods for associating specific sample analytes with spatial locations in the spatial array. Provided herein are methods for preparing a spatial array using a plurality of primers attached to a substrate to guide a plurality of features to specific locations on the spatial array. In a non-limiting example, a plurality of primers on a substrate can be used to guide a plurality of first features that include capture probes onto the substrate. A plurality of second features that are configured to hybridize to the first features and also include capture probes are added to the substrate.

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