公开(公告)号：US20220064630A1

公开(公告)日：2022-03-03

申请号：US17312714

申请日：2019-12-06

Applicant: 10x Genomics, Inc.

Inventor： Zachary Bent ,  Eswar Prasad Ramachandran Iyer ,  Tarjei Sigurd Mikkelsen

IPC: C12N15/10 ,  C12Q1/6837

Abstract: Methods for determining a location of a feature on a spatial array include (a) providing an array of features on a substrate, where a feature of the array includes a barcoded oligonucleotide having, in a 5′ to 3′ direction, a spatial barcode, a cleavage domain, and a constant sequence; (b) hybridizing a priming oligonucleotide to the constant sequence; (c) extending the priming oligonucleotide using the barcoded oligonucleotide as a template; and (d) determining all or a portion of a sequence of the extended priming oligonucleotide corresponding to the spatial barcode, or a complement thereof, and a location of the extended priming oligonucleotide, and using the location of the extended priming oligonucleotide to determine the location of the feature on the spatial array.

公开(公告)号：US20220033888A1

公开(公告)日：2022-02-03

申请号：US17312247

申请日：2019-12-06

Applicant: 10x Genomics, Inc.

Inventor： Michael Schnall-Levin ,  Eswar Prasad Ramachandran Iyer ,  Yifeng Yin ,  Tarjei Sigurd Mikkelsen ,  Preyas Shah ,  Geoffrey McDermott ,  Adam Lowe ,  Joshua Delaney ,  Augusto Manuel Tentori ,  Rajiv Bharadwaj ,  Stefania Giacomello ,  Alexander Gagnon ,  Meghan L. F. Frey ,  Zachary Bent ,  Erik Leonard Henrik Borgstrom

IPC: C12Q1/6837 ,  C12Q1/6881

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

公开(公告)号：US20210230681A1

公开(公告)日：2021-07-29

申请号：US17155764

申请日：2021-01-22

Applicant: 10x Genomics, Inc.

Inventor： David Michael Patterson ,  Sultan Doganay Tuncer ,  Zachary Bent

IPC: C12Q1/6837 ,  C12N9/12 ,  C12N9/00

Abstract: The present disclosure provides methods and compositions for detecting and spatially locating analyte interactions and gene expression in a biological sample. For example, provided herein are methods of determining a location of at least one analyte in a biological sample using analyte-binding moieties, proximity ligation, and an array including capture probes.

公开(公告)号：US10745742B2

公开(公告)日：2020-08-18

申请号：US16230936

申请日：2018-12-21

Applicant: 10X GENOMICS, INC.

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

IPC: C12Q1/68 ,  C40B20/04 ,  C40B50/16 ,  C40B50/18 ,  G06K19/06 ,  C12Q1/6806 ,  C12Q1/6811 ,  C12Q1/6834

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：US20200002763A1

公开(公告)日：2020-01-02

申请号：US16439675

申请日：2019-06-12

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 ,  C12Q1/683 ,  C12Q1/6806

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：US20190383804A1

公开(公告)日：2019-12-19

申请号：US16375119

申请日：2019-04-04

Applicant: 10X Genomics, Inc.

Inventor： Kamila Belhocine ,  Jason Bell ,  Zachary Bent ,  Rajiv Bharadwaj ,  Christopher Hindson ,  Mohammad Rahimi Lenji ,  Bill Kengli Lin ,  Anthony Makarewicz ,  Geoffrey McDermott ,  Elliott Meer ,  Francesca Meschi ,  Tarjei Sigurd Mikkelsen ,  Christopher Joachim O'Keeffe ,  Katherine Pfeiffer ,  Andrew D. Price ,  Paul Ryvkin ,  Michael Schnall-Levin ,  Sarah Taylor ,  Jessica Michele Terry ,  Tobias Daniel Wheeler ,  Yifeng Yin ,  Xinying Zheng ,  Solongo Batjargal Ziraldo ,  Eswar Prasad Ramachandran Iyer ,  Luigi Jhon Alvarado Martinez

IPC: G01N33/53 ,  G01N33/543 ,  C12N15/11

Abstract: 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), genomic DNA, epigenetic information (e.g., accessible chromatin, DNA methylation), and RNA molecules (e.g., mRNA or CRISPR guide RNAs). In some cases, the disclosed methods comprise analysis of analytes from a cell using a cell bead.

公开(公告)号：US20190367969A1

公开(公告)日：2019-12-05

申请号：US16375093

申请日：2019-04-04

Applicant: 10X Genomics, Inc.

Inventor： Kamila Belhocine ,  Jason Bell ,  Zachary Bent ,  Rajiv Bharadwaj ,  Christopher Hindson ,  Mohammad Rahimi Lenji ,  Bill Kengli Lin ,  Anthony Makarewicz ,  Geoffrey McDermott ,  Elliott Meer ,  Francesca Meschi ,  Tarjei Sigurd Mikkelsen ,  Christopher Joachim O'Keeffe ,  Katherine Pfeiffer ,  Andrew D. Price ,  Paul Ryvkin ,  Michael Schnall-Levin ,  Sarah Taylor ,  Jessica Michele Terry ,  Tobias Daniel Wheeler ,  Yifeng Yin ,  Xinying Zheng ,  Solongo Batjargal Ziraldo ,  Eswar Prasad Ramachandran Iyer ,  Luigi Jhon Alvarado Martinez

IPC: C12Q1/6818 ,  C12Q1/6827

Abstract: 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).

公开(公告)号：US20180179591A1

公开(公告)日：2018-06-28

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

CPC classification number: C12Q1/6874 ,  C12N15/1075 ,  C12Q1/6804 ,  C12Q1/6806 ,  C12Q1/683 ,  C12Q2525/191 ,  C12Q2537/143 ,  C12Q2563/179 ,  C12Q2525/179 ,  C12Q2535/122 ,  C12Q2563/131 ,  C12Q2563/149 ,  C12Q2563/159 ,  C12Q2565/543

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：US12297486B2

公开(公告)日：2025-05-13

申请号：US17991309

申请日：2022-11-21

Applicant: 10x Genomics, Inc.

Inventor： David Michael Patterson ,  Sultan Doganay Tuncer ,  Zachary Bent

IPC: C12Q1/68 ,  C12N9/00 ,  C12N9/12 ,  C12Q1/6813 ,  C12Q1/6837 ,  C12Q1/6844

Abstract: The present disclosure provides methods and compositions for detecting and spatially locating analyte interactions and gene expression in a biological sample. For example, provided herein are methods of determining a location of at least one analyte in a biological sample using analyte-binding moieties, proximity ligation, and an array including capture probes.

公开(公告)号：US12054773B2

公开(公告)日：2024-08-06

申请号：US17003790

申请日：2020-08-26

Applicant: 10X GENOMICS, INC.

Inventor： Vijay Kumar Sreenivasa Gopalan ,  Paul Ryvkin ,  Zachary Bent ,  Jessica Michele Terry ,  David Jaffe ,  Patrick Marks ,  Tarjei Sigurd Mikkelsen

IPC: C12Q1/68 ,  C12N15/10 ,  C12Q1/6806 ,  C12Q1/6844 ,  C12Q1/6869

CPC classification number: C12Q1/6869 ,  C12N15/1096 ,  C12Q1/6806 ,  C12Q1/6844

Abstract: The present disclosure provides methods and systems for producing full-length sequencing information of transcriptomes from single cells or from the bulk. Random ligation and circularization of barcoded or non-barcoded complementary deoxyribonucleic molecules can be used to provide a circular template for amplification and subsequent sequencing.