公开(公告)号：US20240218445A1

公开(公告)日：2024-07-04

申请号：US18406946

申请日：2024-01-08

Applicant: 10X Genomics, Inc.

Inventor： Alexander Y. Wong ,  Jeffrey Mellen ,  Kevin Wu ,  Paul Ryvkin

IPC: C12Q1/6881 ,  C07K14/725 ,  C07K16/28 ,  G16B30/00 ,  G16B40/30 ,  G16B45/00 ,  C12Q1/6806 ,  C12Q1/686 ,  C12Q1/6883 ,  G16B30/10

CPC classification number: C12Q1/6881 ,  C07K14/7051 ,  C07K16/2809 ,  G16B30/00 ,  G16B40/30 ,  G16B45/00 ,  C07K2317/565 ,  C12Q1/6806 ,  C12Q1/686 ,  C12Q1/6883 ,  C12Q2600/156 ,  C12Q2600/158 ,  C12Q2600/16 ,  G16B30/10

Abstract: Methods for screening clonotypes are provided. Data representing a plurality of cells from a single subject is obtained. The data represents a plurality of clonotypes. The data includes a plurality of contigs for each respective clonotype in the plurality of clonotypes. Each respective contig in the plurality of contigs comprises (i) an indication of chain type for the respective contig and (ii) a contig sequence of an mRNA of the respective cell. There is determined, using the data, for each respective clonotype in the plurality of clonotypes, a number of the plurality of cells that represent the respective clonotype. In some instances, more than one cell in the plurality of cells have the same clonotype in the plurality of clonotypes. In some instances, the plurality of clonotypes comprises 25 clonotypes and where the plurality of cells includes at least one cell for each clonotype in the plurality of clonotypes.

公开(公告)号：US20210372998A1

公开(公告)日：2021-12-02

申请号：US17209045

申请日：2021-03-22

Applicant: 10X Genomics, Inc.

Inventor： Zahra 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: G01N33/532 ,  C07K14/74 ,  C12N15/85 ,  G01N33/543 ,  G01N33/548 ,  C12N15/10 ,  C12Q1/6804 ,  C12Q1/6806 ,  G01N33/50 ,  G01N33/53 ,  G01N33/58 ,  C12Q1/6818 ,  C12Q1/6827 ,  C12Q1/6881 ,  C12N15/11 ,  G01N33/569

Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and antigen screening. Polynucleotide processing may be useful for a variety of applications. Antigen screening may comprise the use of one or more engineered cells. Engineered cells may be useful for characterizing one or more analytes including, for example, a polypeptide antigen.

公开(公告)号：US20210285044A1

公开(公告)日：2021-09-16

申请号：US16818437

申请日：2020-03-13

Applicant: 10X Genomics, Inc.

Inventor： Paul Ryvkin ,  Jason Underwood ,  Michael Schnall-Levin ,  Tarjei Mikkelsen ,  Benjamin Hindson

IPC: C12Q1/6874 ,  C12Q1/6806 ,  C12Q1/6851

Abstract: Provided herein are compositions, systems and methods for tagging molecular events, reactions, species, etc., but without the need for complex, highly diverse libraries of tagging molecules. Provided are tagging moieties that can have a smaller number, a few, or even a single original “tagging” structure that may be transformed or transformable, in situ, into a collection of larger numbers of unique tagging or “barcode” moieties.

公开(公告)号：US10793905B2

公开(公告)日：2020-10-06

申请号：US16692631

申请日：2019-11-22

Applicant: 10X GENOMICS, INC.

Inventor： Zachary Bent ,  Josephine Harada ,  Christopher Hindson ,  Elliott Meer ,  Tarjei Sigurd Mikkelsen ,  Christopher Joachim O'Keeffe ,  Katherine Pfeiffer ,  Andrew D. Price ,  Paul Ryvkin ,  Serge Saxonov ,  John R. Stuelpnagel ,  Jessica Michele Terry ,  Solongo Batjargal Ziraldo

IPC: C12Q1/68 ,  C12N15/10 ,  C12Q1/6874 ,  C12Q1/683 ,  C12Q1/6804 ,  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：US20200002764A1

公开(公告)日：2020-01-02

申请号：US16443638

申请日：2019-06-17

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：US20180225416A1

公开(公告)日：2018-08-09

申请号：US15891607

申请日：2018-02-08

Applicant: 10X Genomics, Inc.

Inventor： Alexander Y. Wong ,  Jeffrey Mellen ,  Kevin Wu ,  Paul Ryvkin

IPC: G06F19/26 ,  G06F19/24

CPC classification number: G16B45/00 ,  G16B25/00 ,  G16B40/00

Abstract: A visualization system comprising a persistent memory, storing a dataset, and a non-persistent memory implements a pattern visualizing method. The dataset contains discrete attribute values for each first entity in a plurality of first entities for each second entity in a plurality of second entities. The dataset is compressed by blocked compression and represents discrete attribute values in both compressed sparse row and column formats. The discrete attribute values are clustered to assign each second entity to a cluster in a plurality of clusters. Differences in the discrete attribute values for the first entity across the second entities of a given cluster relative to the discrete attribute value for the same first entity across the other clusters are computed thereby deriving differential values. A heat map of these differential values for each first entity for each cluster is displayed to reveal the pattern in the dataset.

公开(公告)号：US20250043346A1

公开(公告)日：2025-02-06

申请号：US18919966

申请日：2024-10-18

Applicant: 10x Genomics, Inc.

Inventor： Paul Ryvkin ,  Jason Underwood ,  Michael Schnall-Levin ,  Tarjei Mikkelsen ,  Benjamin Hindson

IPC: C12Q1/6874 ,  C12Q1/6806 ,  C12Q1/6851

Abstract: Provided herein are compositions, systems and methods for tagging molecular events, reactions, species, etc., but without the need for complex, highly diverse libraries of tagging molecules. Provided are tagging moieties that can have a smaller number, a few, or even a single original “tagging” structure that may be transformed or transformable, in situ, into a collection of larger numbers of unique tagging or “barcode” moieties.

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：US11954614B2

公开(公告)日：2024-04-09

申请号：US16442800

申请日：2019-06-17

Applicant: 10X Genomics, Inc.

Inventor： Alexander Y. Wong ,  Jeffrey Mellen ,  Kevin J. Wu ,  Paul Ryvkin ,  Preyas Shah ,  Patrick Marks ,  Niranjan Srinivas

IPC: G06N7/01 ,  G06F16/28 ,  G06F16/904 ,  G16B25/10 ,  G16B40/00 ,  G16B45/00 ,  G16B50/30

CPC classification number: G06N7/01 ,  G06F16/285 ,  G06F16/904 ,  G16B25/10 ,  G16B40/00 ,  G16B45/00 ,  G16B50/30

Abstract: A visualization system comprising a persistent memory, storing a dataset, and a non-persistent memory implements a pattern visualizing method. The dataset contains discrete attribute values for each first entity of a first type in a plurality of first entities of the first type and discrete attribute values for each first entity of a second type in a plurality of first entities of the second type for each second entity in a plurality of second entities. The dataset is compressed by blocked compression and represents discrete attribute values in both compressed sparse row and column formats. The discrete attribute values are clustered to assign each second entity to a cluster in a plurality of clusters.

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.