公开(公告)号：US10347365B2

公开(公告)日：2019-07-09

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: G16B25/00 ,  G16B40/00 ,  G16B45/00 ,  G06F19/24 ,  G06F19/26 ,  G06F19/20

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：US20180371545A1

公开(公告)日：2018-12-27

申请号：US15984324

申请日：2018-05-19

Applicant: 10X Genomics, Inc.

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

IPC: C12Q1/6881 ,  C07K14/725 ,  C07K16/28

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：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：US20170260584A1

公开(公告)日：2017-09-14

申请号：US15430298

申请日：2017-02-10

Applicant: 10X Genomics, Inc. ,  Fred Hutchinson Cancer Research Center

Inventor： Xinying Zheng ,  Jason H. Bielas ,  Mark T. Gregory ,  Benjamin Hindson ,  Tarjei Sigurd Mikkelsen ,  Ryan Wilson ,  Paul Ryvkin

IPC: C12Q1/68 ,  C12N15/10

CPC classification number: C12Q1/6881 ,  C12N15/1065 ,  C12N15/1093 ,  C12Q2600/156 ,  G01N2015/1006

Abstract: The disclosure provides methods and systems for producing single cell RNA sequencing data. Single nucleotide polymorphisms (SNPs) identified in such data can be used to distinguish subpopulations of cells within a mixed population.

公开(公告)号：US20250117932A1

公开(公告)日：2025-04-10

申请号：US18907230

申请日：2024-10-04

Applicant: 10x Genomics, Inc.

Inventor： Jeffrey Mellen ,  Jeffrey Peck ,  Edward Jaesung Kim DePuy ,  Andreas Girgensohn ,  Paul Ryvkin ,  Elijah Roberts

IPC: G06T7/00

Abstract: Feature pyramiding for in situ data visualizations is provided. In various embodiments, a point cloud is loaded. Each point within the point cloud represents a feature of a biological sample at its corresponding location. At least one tile is determined having a two-dimensional area and a zoom level. Those points having a location within the two-dimensional area are selected from the point cloud. Based on the selected points and the zoom level, a set of display points is determined, each point of the set of display point representing a feature of the biological sample at its corresponding location. The set of display points is provided for display at the zoom level.

公开(公告)号：US20250061732A1

公开(公告)日：2025-02-20

申请号：US18807093

申请日：2024-08-16

Applicant: 10X Genomics, Inc.

Inventor： Dongyao Li ,  Neil Ira Weisenfeld ,  Paul Ryvkin

IPC: G06V20/69 ,  G06V10/26 ,  G06V10/764 ,  G06V10/774

Abstract: Provided herein are methods for image segmentation. An image having a plurality of pixels arranged in a plurality of dimensions is obtained. The image is provided to a pretrained machine learning model and a plurality of amplitudes for each of the plurality of pixel is received from the model. Each of the plurality of amplitudes for each of the plurality of pixels corresponds to exactly one of the plurality of dimensions. At least one instance in the image is identified by: determining a first basin associated with the at least one instance, where the basin consists of a contiguous subset of the plurality of pixels having an amplitude with a magnitude not exceeding first threshold, determining a second subset of the plurality of pixels having an amplitude with a magnitude exceeding the first threshold, where the second subset of pixels bounds the first subset of pixels, and constructing the at least one instance by a flow of the second subset of pixels to the first subset of pixels according to the amplitudes thereof.

公开(公告)号：US20240354607A1

公开(公告)日：2024-10-24

申请号：US18629826

申请日：2024-04-08

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：US12110549B2

公开(公告)日：2024-10-08

申请号：US17822117

申请日：2022-08-24

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

CPC classification number: C12Q1/6874 ,  C12Q1/6806 ,  C12Q1/683 ,  C12Q2525/191 ,  C12Q2537/143 ,  C12Q2563/179

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：US11898206B2

公开(公告)日：2024-02-13

申请号：US15984324

申请日：2018-05-19

Applicant: 10X Genomics, Inc.

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

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

CPC classification number: C12Q1/6881 ,  C07K14/7051 ,  C07K16/2809 ,  G16B30/00 ,  G16B40/30 ,  G16B45/00 ,  C07K2317/565 ,  C12Q1/686 ,  C12Q1/6806 ,  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：US11371094B2

公开(公告)日：2022-06-28

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: C12P19/34 ,  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.