Patents Assigned to 10X GENOMICS, INC.
  • Compositions and methods for sample processing
    Patent number: 11591637
    Abstract: This disclosure provides methods and compositions for sample processing, particularly for sequencing applications. Included within this disclosure are bead compositions, such as diverse libraries of beads attached to large numbers of oligonucleotides containing barcodes. Often, the beads provides herein are degradable. For example, they may contain disulfide bonds that are susceptible to reducing agents. The methods provided herein include methods of making libraries of barcoded beads as well as methods of combining the beads with a sample, such as by using a microfluidic device.
    Type: Grant
    Filed: August 6, 2018
    Date of Patent: February 28, 2023
    Assignee: 10X GENOMICS, INC.
    Inventors: Benjamin Hindson, Christopher Hindson, Michael Schnall-Levin, Kevin Ness, Mirna Jarosz, Donald Masquelier, Serge Saxonov, Landon Merrill, Andrew Price, Paul Hardenbol, Yuan Li
  • Spatially-tagged analyte capture agents for analyte multiplexing
    Patent number: 11592447
    Abstract: Provided herein are methods for preparing biological samples for spatial proteomic analysis, methods of determining a location of a protein analyte in a biological sample, and methods of determining a location of a protein analyte and a nucleic acid analyte in a biological sample.
    Type: Grant
    Filed: May 6, 2022
    Date of Patent: February 28, 2023
    Assignee: 10x Genomics, Inc.
    Inventors: Cedric Uytingco, James Michael Chell, Marlon Stoeckius, Albert Kim, Dulce Ovando Morales, Andrej Hartnett, Yifeng Yin, Jennifer Chew
  • NUCLEIC ACID CONCATEMERS AND METHODS FOR STABILIZING AND/OR COMPACTING THE SAME
    Publication number: 20230057571
    Abstract: The present disclosure in some aspects relates to methods and compositions for accurately detecting and quantifying multiple analytes present in a biological sample. In some aspects, the methods and compositions provided herein address one or more issues associated with the stability and/or size of nucleic acid structures, such as RCPs, in the biological sample without the use of exogenously added oligonucleotide compaction probes. In some embodiments, provided herein are methods involving the use of self-hybridizing hybridizing regions for compacting and/or stabilizing nucleic acid concatemers (e.g., RCPs). In some embodiments, dynamic inter-strand annealing between tandem units of an RCP is used for compaction and/or stabilization. In some embodiments, short palindromic regions in an RCP are used for compaction and/or stabilization.
    Type: Application
    Filed: August 2, 2022
    Publication date: February 23, 2023
    Applicant: 10x Genomics, Inc.
    Inventors: Justin COSTA, Jorge Iván HERNÁNDEZ NEUTA, Patrick J. MARKS
  • Methods for processing nucleic acid molecules
    Patent number: 11584953
    Abstract: The present disclosure provides methods, systems, and kits for processing nucleic acid molecules. A method may comprise providing a template nucleic acid fragment (e.g., within a cell, cell bead, or cell nucleus) within a partition (e.g., a droplet or well) and subjecting the template nucleic acid fragment to one or more processes including a barcoding process and a single primer extension or amplification process. The processed template nucleic acid fragment may then be recovered from the partition and subjected to further amplification to provide material for subsequent sequencing analysis. The methods provided herein may permit simultaneous processing and analysis of both DNA and RNA molecules originating from the same cell, cell bead, or cell nucleus.
    Type: Grant
    Filed: February 12, 2020
    Date of Patent: February 21, 2023
    Assignee: 10X GENOMICS, INC.
    Inventors: Zahra Kamila Belhocine, Jason C. Bell
  • Methods and systems for sample preparation and analysis
    Patent number: 11584954
    Abstract: The present disclosure provides methods and systems for sample preparation and/or analysis. Samples may be cells, or may be derived from one or more cells. Sample preparation may comprise conducting one or more reactions on a target. Such reactions may be conducted in one or more partitions. One or more reactions may be performed in one or more successive operations.
    Type: Grant
    Filed: April 22, 2020
    Date of Patent: February 21, 2023
    Assignee: 10X GENOMICS, INC.
    Inventors: Zahra Kamila Belhocine, Josephine Lee, Francesca Meschi, Luz Montesclaros, Katherine Pfeiffer, Andrew D. Price, Jerald Sapida, David Sukovich, Tobias Daniel Wheeler, Yifeng Yin
  • QUANTITATIVE AND AUTOMATED PERMEABILIZATION PERFORMANCE EVALUATION FOR SPATIAL TRANSCRIPTOMICS
    Publication number: 20230047782
    Abstract: Quantitative methods for optimizing the permeabilization of cellular tissues for spatial transcriptomics are provided. Also provided is an instrument for quantitatively optimizing the permeabilization of cellular tissues used for spatial transcriptomics.
    Type: Application
    Filed: February 5, 2021
    Publication date: February 16, 2023
    Applicant: 10x Genomics, Inc.
    Inventors: Augusto Manuel Tentori, Rajiv Bharadwaj, Hanyoup Kim, Siyuan Xing
  • STABILIZATION AND/OR COMPACTION OF NUCLEIC ACID STRUCTURES
    Publication number: 20230039148
    Abstract: The present disclosure in some aspects relates to methods and compositions for accurately detecting and quantifying multiple analytes present in a biological sample. In some aspects, the methods and compositions provided herein address one or more issues associated with the stability and/or size of nucleic acid structures such as rolling circle amplification products in the biological sample.
    Type: Application
    Filed: August 2, 2022
    Publication date: February 9, 2023
    Applicant: 10x Genomics, Inc.
    Inventor: Toon VERHEYEN
  • COMPOSITIONS AND METHODS FOR ROLLING CIRCLE AMPLIFICATION
    Publication number: 20230044650
    Abstract: The present disclosure in some aspects relates to methods and compositions for accurately detecting and quantifying multiple analytes present in a biological sample. In some aspects, the methods and compositions provided herein address one or more issues associated with the stability and/or size of nucleic acid structures such as rolling circle amplification products in the biological sample.
    Type: Application
    Filed: August 2, 2022
    Publication date: February 9, 2023
    Applicant: 10x Genomics, Inc.
    Inventor: Rhyan Blaine DOCKTER
  • Systems and methods for visualization of single-cell resolution characteristics
    Patent number: 11574706
    Abstract: A dataset is obtained comprising data blocks, each representing a different characteristic, for a plurality of cells across a plurality of bins, each bin representing a different portion of a reference sequence. Cells are clustered on one such characteristic across the bins thereby forming a tree that includes root, intermediate, and terminal nodes, where the cells are terminal nodes and intermediate nodes have daughter nodes, themselves being intermediate nodes or a cell. A subset of the tree is displayed that includes the root and leaves, each leaf representing an intermediate node or a cell. A heat map of the characteristic is also displayed, the map including a segment for each leaf, across the bins. When a segment represents an intermediate node, it is an average of the characteristic across daughters of the node. Graphs of characteristics for the root across the bins are also displayed.
    Type: Grant
    Filed: June 27, 2019
    Date of Patent: February 7, 2023
    Assignee: 10X GENOMICS, INC.
    Inventors: Jeffrey Mellen, Kevin J. Wu, Vijay Kumar Sreenivasa Gopalan, Nicolaus Lance Hepler, Jasper Staab
  • Droplet forming devices and system with differential surface properties
    Patent number: 11565263
    Abstract: Devices, systems, and their methods of use, for generating droplets are provided. One or more geometric parameters of a microfluidic channel can be selected to generate droplets of a desired and predictable droplet size.
    Type: Grant
    Filed: April 6, 2020
    Date of Patent: January 31, 2023
    Assignee: 10x Genomics, Inc.
    Inventors: Rajiv Bharadwaj, Anthony Makarewicz, Bill Kengli Lin
  • Methods for spatial analysis using RNA-templated ligation
    Patent number: 11560593
    Abstract: Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample using RNA-templated ligation.
    Type: Grant
    Filed: March 29, 2022
    Date of Patent: January 24, 2023
    Assignee: 10x Genomics, Inc.
    Inventors: James Michael Chell, Marlon Stoeckius, Jonathan Alles, Caroline Julie Gallant, Christina Galonska, Felice Alessio Bava, Layla Katiraee
  • Method for resetting an array
    Patent number: 11560592
    Abstract: Provided herein are methods for resetting an array to which a biological sample has been applied that include treating the array with a set of biological sample removal conditions.
    Type: Grant
    Filed: December 10, 2021
    Date of Patent: January 24, 2023
    Assignee: 10x Genomics, Inc.
    Inventors: Jennifer Chew, Zachary Bent, Alvaro J Gonzalez Lozano
  • Method of detecting target nucleic acid molecules
    Patent number: 11555219
    Abstract: The present application provides methods for detecting a nucleic acid molecule involving the use of a signal code sequence which corresponds to said nucleic acid molecule and a plurality of labelled detection probes which yield signals which make up the signal code sequence. In particular, the invention provides a sequential barcoding and decoding scheme which utilises a sequencing-by-hybridisation (SBH) strategy to sequence and decode a nucleotide barcode sequence, and to differentiate the nucleotide barcode sequence from other nucleotide barcode sequences. In an extension of the method, the application also provides a new coding scheme for providing a target nucleic acid with a detectable “colour” (or similar signal)-based code.
    Type: Grant
    Filed: June 1, 2021
    Date of Patent: January 17, 2023
    Assignee: 10x Genomics, Inc.
    Inventors: Malte Kühnemund, Toon Verheyen
  • Methods for spatial analysis using targeted RNA depletion
    Patent number: 11535887
    Abstract: Provided herein are methods for spatial analysis using targeted RNA depletion.
    Type: Grant
    Filed: December 9, 2021
    Date of Patent: December 27, 2022
    Assignee: 10x Genomics, Inc.
    Inventors: Caroline Julie Gallant, Linda Kvastad
  • REVERSE TRANSCRIPTASE VARIANTS
    Publication number: 20220403350
    Abstract: The application provides compositions including engineered reverse transcriptases with at least one altered reverse-transcriptase related activity. The engineered reverse transcriptases or reverse transcription enzymes unexpectedly exhibit one or more altered reverse transcriptase related activities such as but not limited to altered template switching efficiency, altered transcription efficiency or both.
    Type: Application
    Filed: June 10, 2022
    Publication date: December 22, 2022
    Applicant: 10X Genomics, Inc.
    Inventors: Sonya A. CLARK, Derek Hunter Vallejo, Carolina Cuellar, Katherine Pfeiffer
  • METHODS FOR ENRICHING NUCLEIC ACID LIBRARIES FOR TARGET MOLECULES THAT DO NOT PRODUCE ARTEFACTUAL ANTISENSE READS
    Publication number: 20220403375
    Abstract: Provided herein are methods for enrichment of nucleic acid libraries for non-artefactual on-target molecules that produce bona fide sequencing reads while eliminating or reducing artefactual on-target molecules that produce wasted reads thereby improving sequencing efficiency. Methods comprise the neutralization of a single artefactual strand of a dsDNA molecule and capture of the non-artefactual strand thereby generating enriched sequencing libraries.
    Type: Application
    Filed: June 3, 2022
    Publication date: December 22, 2022
    Applicant: 10x Genomics, Inc.
    Inventor: Luigi Jhon Alvarado Martinez
  • Method for transposase-mediated spatial tagging and analyzing genomic DNA in a biological sample
    Patent number: 11519033
    Abstract: The present disclosure relates to materials and methods for spatially analyzing nucleic acids that have been fragmented with a transposase enzyme, alone or in combination with other types of analytes.
    Type: Grant
    Filed: March 7, 2022
    Date of Patent: December 6, 2022
    Assignee: 10x Genomics, Inc.
    Inventors: Michael Schnall-Levin, Michael Ybarra Lucero, Tarjei Sigurd Mikkelsen, Patrik Stahl, Jonas Frisen, Maja Marklund, Enric Llorens Bobadilla
  • Systems and methods for identifying morphological patterns in tissue samples
    Patent number: 11514575
    Abstract: A discrete attribute value dataset is obtained that is associated with a plurality of probe spots each assigned a different probe spot barcode. The dataset comprises spatial projections, each comprising images of a biological sample. Each image includes a corresponding plurality of discrete attribute values for the probe spots. Each such value is associated with a probe spot in the plurality of probes spots based on the probe spot barcodes. The dataset is clustered using the discrete attribute values, or dimension reduction components thereof, for a plurality of loci at each respective probe spot across the images of the projections thereby assigning each probe spot to a cluster in a plurality of clusters. Morphological patterns are identified from the spatial arrangement of the probe spots in the various clusters.
    Type: Grant
    Filed: September 30, 2020
    Date of Patent: November 29, 2022
    Assignee: 10X GENOMICS, INC.
    Inventors: Jeffrey Clark Mellen, Jasper Staab, Kevin J. Wu, Neil Ira Weisenfeld, Florian Baumgartner, Brynn Claypoole
  • Nucleic acid library methods
    Patent number: 11512308
    Abstract: Provided herein are methods, compositions, and kits for removing a portion of a sequence in a member of a nucleic acid library.
    Type: Grant
    Filed: March 9, 2022
    Date of Patent: November 29, 2022
    Assignee: 10x Genomics, Inc.
    Inventors: Caroline Julie Gallant, Marlon Stoeckius, Katherine Pfeiffer
  • Methods for spatial analysis using RNA-templated ligation
    Patent number: 11505828
    Abstract: Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample using RNA-templated ligation.
    Type: Grant
    Filed: April 1, 2021
    Date of Patent: November 22, 2022
    Assignee: 10x Genomics, Inc.
    Inventors: James Michael Chell, Marlon Stoeckius, Jonathan Alles, Caroline Julie Gallant, Christina Galonska, Layla Katiraee