Patents Assigned to 10X GENOMICS, INC.
  • Multiplex capture of gene and protein expression from a biological sample
    Patent number: 11739381
    Abstract: Provided herein are methods, compositions, and kits for preparing biological samples for multiplex spatial gene expression and proteomic analysis, such as determining a location of a nucleic acid analyte and a protein analyte in a biological sample.
    Type: Grant
    Filed: July 18, 2022
    Date of Patent: August 29, 2023
    Assignee: 10x Genomics, Inc.
    Inventors: Jennifer Chew, Joseph Francis Shuga, Patrick Roelli, Denise Cheung, Alexander Hermes, Yifeng Yin, Naishitha Anaparthy, Ryo Hatori, Marlon Stoeckius, Rapolas Spalinskas, Anna-Maria Katsori, Cedric Uytingco, Mesruh Turkekul, David Sukovich, Christina Galonska, Aleksandra Jurek, Octavian Marian Bloju
  • Methods and compositions for targeted nucleic acid sequencing
    Patent number: 11739368
    Abstract: The present invention is directed to methods, compositions and systems for capturing and analyzing sequence information contained in targeted regions of a genome. Such targeted regions may include exomes, partial exomes, introns, combinations of exonic and intronic regions, genes, panels of genes, and any other subsets of a whole genome that may be of interest.
    Type: Grant
    Filed: October 6, 2020
    Date of Patent: August 29, 2023
    Assignee: 10X GENOMICS, INC.
    Inventors: Mirna Jarosz, Michael Schnall-Levin, Serge Saxonov, Benjamin J. Hindson, Xinying Zheng
  • Methods and systems for analysis of chromatin
    Patent number: 11739440
    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).
    Type: Grant
    Filed: June 9, 2020
    Date of Patent: August 29, 2023
    Assignee: 10X GENOMICS, INC.
    Inventors: Jason Bell, Geoffrey McDermott, Francesca Meschi, Katherine Pfeiffer, Michael Schnall-Levin, Xinying Zheng
  • Spatial assays with perturbed cells
    Patent number: 11732299
    Abstract: This disclosure relates to methods for spatial profiling of analytes present in a biological sample. Also provided are methods for using spatially barcoded arrays to detect a biological analyte in a cell comprising a small molecule.
    Type: Grant
    Filed: January 20, 2021
    Date of Patent: August 22, 2023
    Assignee: 10x Genomics, Inc.
    Inventor: Eswar Prasad Ramachandran Iyer
  • Methods and systems for processing polynucleotides
    Patent number: 11732302
    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.
    Type: Grant
    Filed: June 2, 2022
    Date of Patent: August 22, 2023
    Assignee: 10X Genomics, Inc.
    Inventors: Phillip Belgrader, Josephine Harada, Tarjei Sigurd Mikkelsen, Katherine Pfeiffer, Serge Saxonov, John R. Stuelpnagel
  • Increasing efficiency of spatial analysis in a biological sample
    Patent number: 11732300
    Abstract: Disclosed herein are methods of amplifying an analyte in a biological sample using a bridging oligonucleotide that hybridizes to a captured analyte. The methods disclosed herein include steps of (a) contacting a biological sample with a substrate having capture probes comprising a capture domain and a spatial barcode; (b) hybridizing the analyte to the capture domain; and (c) contacting the analyte to a bridging oligonucleotide comprising (i) a capture-probe-binding sequence, and (ii) an analyte-binding sequence; (d) extending the bridging oligonucleotide; and (e) determining (i) all or a part of the sequence of the analyte, or a complement thereof, and (ii) the spatial barcode, or a complement thereof, and using the determined sequence of (i) and (ii) to determine the location of the analyte in the biological sample.
    Type: Grant
    Filed: February 4, 2021
    Date of Patent: August 22, 2023
    Assignee: 10x Genomics, Inc.
    Inventor: Felice Alessio Bava
  • Methods and systems for nucleic acid preparation and chromatin analysis
    Patent number: 11725231
    Abstract: The present disclosure provides methods and systems for nucleic acid preparation and/or analysis. Nucleic acids may be derived from one or more cells. Nucleic acid preparation may comprise generating nucleic acid molecules of varying lengths. Nucleic acid analysis may comprise identifying nucleic acid sequence information with nucleosome position information.
    Type: Grant
    Filed: April 21, 2020
    Date of Patent: August 15, 2023
    Assignee: 10x Genomics, Inc.
    Inventor: Geoffrey McDermott
  • METHODS AND COMPOSITIONS FOR ROLLING CIRCLE AMPLIFICATION
    Publication number: 20230242974
    Abstract: The present disclosure in some aspects relates to methods and compositions for detecting and quantifying multiple analytes present in a biological sample by rolling circle amplification (RCA). In some aspects, the methods and compositions provided herein address issues associated with control of signal spot size and intensity for RCA products (RCPs) in a sample. In some aspects, provided herein are methods and compositions (e.g., probes and/or reaction mixtures) for slowing down RCA and/or decreasing the size of RCA products. In some embodiments, nucleotides or nucleotide analogs having a hydrophobic group (e.g., a hydrophobic modification on the base) are included in nucleotides for RCA and incorporated into the RCP product, leading to reduction of RCP size without the need of crosslinking an incorporated hydrophobic nucleotide or nucleotide analog to the RCP itself or another molecule.
    Type: Application
    Filed: December 23, 2022
    Publication date: August 3, 2023
    Applicant: 10x Genomics, Inc.
    Inventors: Justin COSTA, Jorge Iván HERNÁNDEZ NEUTA
  • Methods and systems for processing polynucleotides
    Patent number: 11713457
    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.
    Type: Grant
    Filed: November 14, 2022
    Date of Patent: August 1, 2023
    Assignee: 10X GENOMICS, INC.
    Inventors: Benjamin Hindson, Christopher Hindson, Michael Schnall-Levin, Kevin Ness, Mirna Jarosz, Serge Saxonov
  • Methods and systems for cell and bead processing
    Patent number: 11703427
    Abstract: The present disclosure provides methods and systems for cell and bead processing or analysis. A method for processing a cell or bead may include subjecting a bead to conditions sufficient to change a first characteristic or set of characteristics (e.g., cell or bead size). Such a method may further include subjecting the cell or bead to conditions sufficient to change a second characteristic or set of characteristics. In some cases, crosslinks may be formed within the cell or bead.
    Type: Grant
    Filed: June 7, 2019
    Date of Patent: July 18, 2023
    Assignee: 10X GENOMICS, INC.
    Inventors: Christopher Hindson, Andrew D. Price, Michael Schnall-Levin
  • Methods and devices for magnetic separation
    Patent number: 11701668
    Abstract: Devices, systems, and their methods of use, for sorting or separating magnetic particles are provided. A magnetic source, e.g., with at least one sharp feature, can be employed to exert a strong magnetic field on magnetic particles in order to separate particles of a desired and predictable property.
    Type: Grant
    Filed: May 7, 2021
    Date of Patent: July 18, 2023
    Assignee: 10x Genomics, Inc.
    Inventor: Alireza Salmanzadeh
  • Methods for printing cells and generating arrays of barcoded cells
    Patent number: 11702693
    Abstract: This disclosure relates to compositions and methods for analyzing single cells using cell printing and spatial analysis.
    Type: Grant
    Filed: January 19, 2021
    Date of Patent: July 18, 2023
    Assignee: 10x Genomics, Inc.
    Inventor: Rajiv Bharadwaj
  • Enhancing specificity of analyte binding
    Patent number: 11702698
    Abstract: Methods for enhancing specificity of an analyte binding moiety or probe oligonucleotide to an analyte are provided herein. For example, methods provided herein include blocking a capture binding domain, thereby preventing hybridization to the capture domain of the capture probe affixed to a substrate. Further methods include releasing the block from the capture binding domain, thereby allowing the capture binding domain to specifically bind to the capture domain of the capture probe on the substrate.
    Type: Grant
    Filed: January 11, 2022
    Date of Patent: July 18, 2023
    Assignee: 10x Genomics, Inc.
    Inventor: Marlon Stoeckius
  • Spatial transcriptomics for antigen-receptors
    Patent number: 11692218
    Abstract: Provided herein are methods, compositions, and kits for the detection of immune cell clonotypes and immune cell analytes within a biological sample.
    Type: Grant
    Filed: December 15, 2021
    Date of Patent: July 4, 2023
    Assignee: 10x Genomics, Inc.
    Inventors: Camilla Engblom, Kim Thrane, Jeffrey Mold, Jonas Frisen, Joakim Lundeberg, Qirong Lin
  • Methods, compositions, and systems for spatial analysis of analytes in a biological sample
    Patent number: 11680260
    Abstract: Provided herein are methods for capturing a connected probe and/or a capture handle sequence to a capture domain of a capture probe.
    Type: Grant
    Filed: October 28, 2022
    Date of Patent: June 20, 2023
    Assignee: 10x Genomics, Inc.
    Inventors: Hanyoup Kim, David Sukovich, Layla Katiraee, Augusto Manuel Tentori, Lauren Gutgesell, Janine Hensel, Seayar Mohabbat
  • RESTRICTION DIGEST BASED SEQUENTIAL DECODING
    Publication number: 20230183787
    Abstract: The present application provides methods and compositions for analyzing biological samples involving sequential decoding of barcode regions of nucleic acid probes, wherein the barcode regions comprise barcode sequences that define a sequential signal code. In particular, the present application provides a method wherein probe hybridization generates a double-stranded recognition site for a nuclease. Cleavage of the double-stranded recognition site releases a sequence associated with the probe, thus releasing a detectable label associated with the probe.
    Type: Application
    Filed: December 12, 2022
    Publication date: June 15, 2023
    Applicant: 10x Genomics, Inc.
    Inventors: Felice Alessio BAVA, Toon VERHEYEN
  • COMPOSITIONS AND METHODS FOR ISOLATING NUCLEIC ACID MOLECULES
    Publication number: 20230167496
    Abstract: This invention provides methods, compositions, kits and systems for isolating and/or enriching nucleic acid molecules. In some aspects, this disclosure provides methods for enriching nucleic acid molecules that can be used for transcriptomics. Methods of this invention can detect nucleic acid molecules of a sample that may be masked by highly expressed molecules.
    Type: Application
    Filed: September 30, 2022
    Publication date: June 1, 2023
    Applicant: 10x Genomics, Inc.
    Inventor: Felice Alessio BAVA
  • Methods for sorting particles
    Patent number: 11660601
    Abstract: Methods and systems for sorting particles are provided. Methods and systems for sorting cell beads are provided. In some cases, cell beads may be sorted from particles unoccupied with cell derivatives. In some cases, singularly occupied cell beads may be sorted from unoccupied particles and multiply occupied cell beads.
    Type: Grant
    Filed: June 28, 2022
    Date of Patent: May 30, 2023
    Assignee: 10x Genomics, Inc.
    Inventors: Rajiv Bharadwaj, Michael Schnall-Levin, Anthony Makarewicz, Steven Short
  • Spatial analysis of DNA methylation
    Patent number: 11661626
    Abstract: Provided herein are methods of identifying a methylation status of an analyte in a biological sample. Also provided herein are methods that combine identifying the methylation status with spatial technology to identify the location of a methylation status in a biological sample.
    Type: Grant
    Filed: August 5, 2022
    Date of Patent: May 30, 2023
    Assignee: 10x Genomics, Inc.
    Inventors: Layla Katiraee, Michael Schnall-Levin, Christina Galonska, Marlon Stoeckius
  • Cartridge with sample holder
    Patent number: D996644
    Type: Grant
    Filed: August 5, 2021
    Date of Patent: August 22, 2023
    Assignee: 10x Genomics, Inc.
    Inventors: Alexander Post Kindwall, David Morgan, Jennifer Lew, Joaquin Trosper-Torres, Kevin Gilmartin, Liza S. Man