公开(公告)号：US10323278B2

公开(公告)日：2019-06-18

申请号：US15875899

申请日：2018-01-19

Applicant: 10X GENOMICS, INC.

Inventor： Phillip Belgrader ,  Zachary Bent ,  Tarjei Sigurd Mikkelsen ,  Paul Ryvkin ,  Jessica Michele Terry

IPC: C12Q1/68 ,  C12Q1/6874 ,  C12Q1/683 ,  C12Q1/6806

Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing.

公开(公告)号：US20250154569A1

公开(公告)日：2025-05-15

申请号：US19023801

申请日：2025-01-16

Applicant: 10x Genomics, Inc.

Inventor： Marlon Stoeckius ,  Stefania Giacomello ,  Zachary Bent ,  Meghan L. F. Frey ,  Alexander Gagnon ,  Erik Leonard Henrik Borgstrom

IPC: C12Q1/6837

Abstract: The present disclosure relates to compositions, methods, and kits for generating capture probes on a substrate for identifying the location of analytes in a biological sample.

公开(公告)号：US20250027150A1

公开(公告)日：2025-01-23

申请号：US18786209

申请日：2024-07-26

Applicant: 10x Genomics, Inc.

Inventor： Phillip Belgrader ,  Zachary Bent ,  Rajiv Bharadwaj ,  Vijay Kumar Sreenivasa Gopalan ,  Josephine Harada ,  Christopher Hindson ,  Mohammad Rahimi Lenji ,  Michael Ybarra Lucero ,  Geoffrey McDermott ,  Elliott Meer ,  Tarjei Sigurd Mikkelsen ,  Christopher Joachim O'Keeffe ,  Katherine Pfeiffer ,  Andrew D. Price ,  Paul Ryvkin ,  Serge Saxonov ,  John R. Stuelpnagel ,  Jessica Michele Terry ,  Tobias Daniel Wheeler ,  Indira Wu ,  Solongo Batjargal Ziraldo ,  Stephane Claude Boutet ,  Sarah Taylor ,  Niranjan Srinivas

IPC: C12Q1/6874 ,  C12Q1/6806 ,  C12Q1/683

Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and analyte characterization. Such polynucleotide processing may be useful for a variety of applications, including analyte characterization by polynucleotide sequencing. 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), genomic DNA, and RNA (e.g., mRNA or CRISPR guide RNAs). Also described herein, are barcoded labelling agents and oligonucleotide molecules useful for “tagging” analytes for characterization.

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：US11884962B2

公开(公告)日：2024-01-30

申请号：US17095578

申请日：2020-11-11

Applicant: 10X GENOMICS, INC.

Inventor： Zachary Bent ,  Elliott Meer ,  Daniel Riordan ,  Paul Ryvkin ,  Niranjan Srinivas ,  Jessica Terry ,  Alex Gagnon

IPC: C12Q1/6806 ,  C12Q1/6811 ,  C12Q1/6834 ,  C40B20/04 ,  C40B50/16 ,  C40B50/18 ,  G06K19/06

CPC classification number: C12Q1/6806 ,  C12Q1/6811 ,  C12Q1/6834 ,  C40B20/04 ,  C40B50/16 ,  C40B50/18 ,  G06K19/06093 ,  C12Q1/6806 ,  C12Q2521/319 ,  C12Q2521/501 ,  C12Q2525/155 ,  C12Q2525/191 ,  C12Q2535/122 ,  C12Q2563/149 ,  C12Q2563/159 ,  C12Q2563/179 ,  C12Q2565/537 ,  C12Q2565/629

Abstract: The present disclosure provides methods of generating supports (e.g., beads) comprising barcode molecules coupled thereto. A barcode molecule coupled to a support may comprise a barcode sequence and a functional sequence. A barcode molecule may be generated using two or more ligation reactions in a combinatorial fashion. A support comprising two or more different barcode molecules may be useful for analyzing or processing one or more analytes such as nucleic acid molecules, proteins, and/or perturbation agents.

公开(公告)号：US11821035B1

公开(公告)日：2023-11-21

申请号：US17162991

申请日：2021-01-29

Applicant: 10x Genomics, Inc.

Inventor： Zachary Bent ,  Marlon Stoeckius

IPC: C12Q1/6876

CPC classification number: C12Q1/6876

Abstract: Provided herein are methods of detecting target nucleic acids and uses of the same.

公开(公告)号：US20230167433A1

公开(公告)日：2023-06-01

申请号：US18049880

申请日：2022-10-26

Applicant: 10x Genomics, Inc.

Inventor： Augusto Manuel Tentori ,  Zachary Bent ,  Rajiv Bharadwaj

IPC: C12N15/10 ,  C12Q1/6874

CPC classification number: C12N15/1065 ,  C12Q1/6874

Abstract: Methods and systems for processing nucleic acids and identifying the presence of a barcode multiplet event are disclosed. The methods and systems generally may comprise the presence of a support comprising multiplet probe molecules which may be used to interact with other barcode molecule to generate molecules that comprise multiple barcode sequences. The methods and systems can be applied to a variety of biological samples and can analyze different nucleic acids, proteins, or other macromolecules of the biological samples.

公开(公告)号：US20220403455A1

公开(公告)日：2022-12-22

申请号：US17891641

申请日：2022-08-19

Applicant: 10x Genomics, Inc.

Inventor： Eswar Prasad Ramachandran Iyer ,  Zachary Bent ,  Yifeng Yin ,  Eileen Dalin

IPC: C12Q1/6837 ,  C12Q1/6841

Abstract: Provided herein are methods of determining a location of a target analyte in a non-permeabilized biological sample that include the use of a blocking probe.

公开(公告)号：US20210324457A1

公开(公告)日：2021-10-21

申请号：US17271866

申请日：2019-08-27

Applicant: Eswar Prasad RAMACHANDRAN IYER ,  Michael SCHNALL-LEVIN ,  Augusto Manuel TENTORI ,  Tarje Sigurd MIKKELSEN ,  Benjamin HINDSON ,  Michael Ybarra LUCERO ,  Rajiv BHARADWAJ ,  Yifeng YIN ,  Zachary BENT ,  Jennifer CHEW ,  Meghan L. F. FREY ,  Linda KVASTAD ,  Joakim LUNDEBERG ,  Eva Gracia VILLACAMPA ,  10x Genomics, Inc.

Inventor： Eswar Prasad Ramachandran Iyer ,  Michael Schnall-Levin ,  Augusto Manuel Tentori ,  Tarjei Sigurd Mikkelsen ,  Benjamin Hindson ,  Michael Ybarra Lucero ,  Rajiv Bharadwaj ,  Yifeng Yin ,  Zachary Bent ,  Jennifer Chew ,  Meghan L. F. Frey ,  Linda Kvastad ,  Joakim Lundeberg ,  Eva Gracia Villacampa

IPC: C12Q1/6837 ,  C12Q1/6841

Abstract: This disclosure relates to methods for generating spatially barcoded arrays using concentration gradients.

公开(公告)号：US20210155982A1

公开(公告)日：2021-05-27

申请号：US16951864

申请日：2020-11-18

Applicant: 10X Genomics, Inc.

Inventor： Yifeng Yin ,  Zachary Bent ,  Stephen Williams ,  Ian Fiddes ,  Jeffrey Clark Mellen ,  Jasper Staab ,  Kevin J. Wu ,  Neil Ira Weisenfeld ,  Florian Baumgartner ,  Brynn Claypoole ,  Preyas Shah ,  Narek Dshkhunyan ,  Erik Leonard Henrik Borgstrom ,  Benjamin McCreath

IPC: C12Q1/6869 ,  C12Q1/6837 ,  G06T7/194 ,  G06T7/13 ,  G06T7/00 ,  G06N5/00

Abstract: Systems and methods for spatial analysis of analytes include placing a sample on a substrate having fiducial markers and capture spots. Then, an image of the sample is acquired and sequence reads are obtained from the capture spots. Each capture probe plurality in a set of capture probe pluralities is (i) at a different capture spot, (ii) directly or indirectly associates with analytes from the sample and (iii) has a unique spatial barcode. The sequencing reads serve to detect the analytes. Sequencing reads include a spatial barcode of the corresponding capture probe plurality. Spatial barcodes localize reads to corresponding capture spots, thereby dividing them into subsets, each subset for a respective capture spot. Fiducial markers facilitate a composite representation comprising (i) the image aligned to the capture spots and (ii) a representation of each subset of sequence reads at respective positions within the image mapping to the corresponding capture spots.