公开(公告)号：US20210237022A1

公开(公告)日：2021-08-05

申请号：US17161007

申请日：2021-01-28

Applicant: 10X Genomics, Inc.

Inventor： Felice Alessio Bava

IPC: B01J19/00

Abstract: Disclosed are extended and/or branched oligonucleotide capture probe assemblies for use in spatial transcriptomics systems, and methods for making the capture probe assemblies.

公开(公告)号：US12180543B2

公开(公告)日：2024-12-31

申请号：US17312375

申请日：2019-12-06

Applicant: 10x Genomics, Inc.

Inventor： Cedric Uytingco ,  Zachary Bent ,  Eswar Prasad Ramachandran Iyer ,  Fernandino Valdecanas ,  Meghan L. F. Frey ,  Steven William Short ,  Yifeng Yin ,  Rajiv Bharadwaj ,  Joakim Lundeberg ,  Augusto Manuel Tentori ,  David Maurice Cox ,  Jennifer Chew ,  Felice Alessio Bava ,  Linda Kvastad ,  Andrew D. Price

IPC: C12Q1/6844 ,  B01L3/00 ,  B01L9/00 ,  C12N15/10 ,  C12Q1/6837 ,  C12Q1/6841 ,  C12Q1/6855 ,  C12Q1/6869 ,  C12Q1/6874 ,  C12Q1/6876 ,  C12Q1/6881 ,  G01N21/64 ,  G01N33/483 ,  G01N35/00 ,  G02B21/16 ,  G02B21/26 ,  G02B21/34 ,  G02B21/36

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.

公开(公告)号：US20240401117A1

公开(公告)日：2024-12-05

申请号：US18804654

申请日：2024-08-14

Applicant: 10x Genomics, Inc.

Inventor： Felice Alessio Bava

IPC: 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.

公开(公告)号：US12031177B1

公开(公告)日：2024-07-09

申请号：US17338031

申请日：2021-06-03

Applicant: 10x Genomics, Inc.

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

IPC: C12Q1/6841

CPC classification number: C12Q1/6841

Abstract: Provided herein are methods of enhancing spatial resolution of an analyte using sandwich maker system. The methods and systems used herein include a first substrate that includes a plurality of probes that include poly-thymine sequence and a second substrate that includes a plurality of probes comprising a capture domain and a spatial domain.

公开(公告)号：US20240182968A1

公开(公告)日：2024-06-06

申请号：US18438896

申请日：2024-02-12

Applicant: 10x Genomics, Inc.

Inventor： Felice Alessio Bava

IPC: C12Q1/6876 ,  C12Q1/6837

CPC classification number: C12Q1/6876 ,  C12Q1/6837 ,  C12Q2521/507 ,  C12Q2525/173 ,  C12Q2531/125 ,  C12Y605/01001 ,  C12Y605/01003

Abstract: This disclosure relates to methods for increasing capture efficiency of a spatial array using rolling circle amplification of a padlock probe that hybridizes to a capture probe. Also provided are methods for using such spatial arrays to detect a biological analyte in a biological sample.

公开(公告)号：US20240150812A1

公开(公告)日：2024-05-09

申请号：US18388753

申请日：2023-11-10

Applicant: 10x Genomics, Inc.

Inventor： Felice Alessio Bava ,  Geoffrey McDermott

IPC: C12Q1/6806 ,  C12N15/10

CPC classification number: C12Q1/6806 ,  C12N15/1013

Abstract: Disclosed are methods, compositions and kits for contacting a sample containing a biological particle with a catalyst associated with or attached to a support. The biological particle may be cells and/or nuclei. The catalyst may be an enzyme configured to digest an extracellular molecule, such as an extracellular biological molecule, including extracellular nucleic acid molecules. In some examples, the biological particle is an aggregate of cells that is processed to single cells with a nuclease that is attached to a bead support. The bead and nuclease may subsequently be removed from the system. The single cells that result from the method can be used in single cell-based droplet systems for obtaining genome or transcriptome profiles of single cells.

公开(公告)号：US11933957B1

公开(公告)日：2024-03-19

申请号：US18175082

申请日：2023-02-27

Applicant: 10x Genomics, Inc.

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

IPC: G02B21/26 ,  G01N33/483 ,  G01N35/00 ,  G02B21/34 ,  G02B21/36

CPC classification number: G02B21/26 ,  G01N33/4833 ,  G01N35/00732 ,  G02B21/34 ,  G02B21/365 ,  G01N2035/00752

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.

公开(公告)号：US20240033743A1

公开(公告)日：2024-02-01

申请号：US18245855

申请日：2021-09-17

Applicant: 10x Genomics, Inc.

Inventor： Augusto Manuel Tentori ,  Hanyoup Kim ,  Siyuan Xing ,  Rajiv Bharadwaj ,  Bill Kengli Lin ,  Felice Alessio Bava ,  Pratomo Putra Alimsijah ,  Hendricus Marindra ,  Spontaneous Rose Mcknight Russell ,  Nabil Mikhaiel

IPC: B01L9/00

CPC classification number: B01L9/52 ,  B01L2200/025 ,  B01L2300/027 ,  B01L2300/0822 ,  B01L2300/1883 ,  B01L7/52

Abstract: A sample holder is provided. The sample holder includes a first member including a first retaining mechanism configured to retain a first substrate comprising a sample. The first retaining mechanism configured to retain the first substrate disposed in a first plane. The sample holder further includes a second member including a second retaining mechanism configured to retain a second substrate including a reagent medium disposed in a second plane. The sample holder further includes an alignment mechanism connected to one or both of the first member and the second member. The alignment mechanism configured to align the first and second members along the first plane and/or the second plane such that the sample contacts at least a portion of the reagent medium when the first and second members are aligned and within a threshold distance along an axis orthogonal to the second plane.

公开(公告)号：US20230416808A1

公开(公告)日：2023-12-28

申请号：US18243582

申请日：2023-09-07

Applicant: 10x Genomics, Inc.

Inventor： David Sukovich ,  Felice Alessio Bava ,  Augusto Manuel Tentori ,  Hanyoup Kim ,  Amanda Janesick

IPC: C12Q1/6841

CPC classification number: C12Q1/6841

Abstract: Provided herein are methods, compositions, and systems for improved in situ detection of analytes and spatial analysis using, e.g., a sequencing readout.

公开(公告)号：US20230267625A1

公开(公告)日：2023-08-24

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: G06T7/33 ,  G06V10/25

CPC classification number: G06T7/33 ,  G06V10/25 ,  G06T2207/10056 ,  G06T2207/20132

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 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.