Patents Assigned to 10X GENOMICS, INC.
  • GENERATING CAPTURE PROBES FOR SPATIAL ANALYSIS
    Publication number: 20220033888
    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.
    Type: Application
    Filed: December 6, 2019
    Publication date: February 3, 2022
    Applicant: 10x Genomics, Inc.
    Inventors: 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
  • METHODS OF USING MASTER / COPY ARRAYS FOR SPATIAL DETECTION
    Publication number: 20220025446
    Abstract: This disclosure provides methods for spatial profiling of biological analytes present in a biological sample. Methods include generating feature arrays using a master/copy format using recessed arrays, and methods for using such arrays. For example spatially-tagged analyte capture analytes can be used in spatial detection in methods to determine the location of analytes (e.g., proteins) in biological samples.
    Type: Application
    Filed: December 6, 2019
    Publication date: January 27, 2022
    Applicant: 10x Genomics, Inc.
    Inventor: Preyas Shah
  • GENERATING SPATIAL ARRAYS WITH GRADIENTS
    Publication number: 20220025447
    Abstract: The present disclosure relates to materials and methods for generating spatial arrays with gradients and using the generated spatial arrays to identify the location of analytes present in a biological sample.
    Type: Application
    Filed: December 6, 2019
    Publication date: January 27, 2022
    Applicant: 10x Genomics, Inc.
    Inventors: Augusto Manuel Tentori, Marlon Stoeckius
  • THREE-DIMENSIONAL SPATIAL ANALYSIS
    Publication number: 20220017951
    Abstract: This disclosure relates to compositions and methods for three-dimensional spatial profiling of analytes in a biological sample.
    Type: Application
    Filed: March 20, 2020
    Publication date: January 20, 2022
    Applicant: 10x Genomics, Inc.
    Inventors: Eswar Prasad Ramachandran Iyer, Tarjei Sigurd Mikkelsen
  • NUCLEIC ACID ASSAYS USING CLICK CHEMISTRY BIOCONJUGATION
    Publication number: 20210388423
    Abstract: Provided herein are methods of sequencing comprising click chemistry bioconjugation. In some embodiments, target polynucleotide sequences on the same or different molecules are contacted with and hybridize to probes comprising click functional groups. Probes (e.g., reading probes) hybridizing to adaptor sequences adjacent to different sequences of interest (e.g., barcodes to be sequenced) can be hybridized simultaneously in large pools. In some embodiments, the provided methods achieve multiplexing without requiring separate hybridization of probes (e.g., reading probes) for each sequencing-by-ligation cycle, thereby reducing total hybridization time which is typically a most time-consuming step in in situ technologies. In some aspects, the hybridized probes (e.g., reading probes) are clicked onto detectable probes to analyze a sequence of a target polynucleotide in a sequencing-by-ligation fashion.
    Type: Application
    Filed: June 11, 2021
    Publication date: December 16, 2021
    Applicant: 10x Genomics, Inc.
    Inventors: Felice Alessio BAVA, David M. PATTERSON, Meiliana TJANDRA, Yi LUO
  • METHODS FOR ANALYZING TARGET NUCLEIC ACIDS AND RELATED COMPOSITIONS
    Publication number: 20210388424
    Abstract: The present disclosure, among other things, provides methods for analyzing a target nucleic acid in a biological sample. In some aspects, the methods involve the use of a set of probe polynucleotides, for example comprising three polynucleotides, for assessing target nucleic acids. In some aspects, the presence, amount and/or sequence of the target nucleic acid is analyzed in situ. In some aspects, the methods involve anchoring or linking a portion of the set of polynucleotides to a scaffold or other nucleic acids. Also provided are polynucleotides, set of polynucleotides, compositions, kits, devices and systems for use in accordance with the methods.
    Type: Application
    Filed: June 11, 2021
    Publication date: December 16, 2021
    Applicant: 10x Genomics, Inc.
    Inventor: Felice Alessio BAVA
  • Single cell analysis of transposase accessible chromatin
    Patent number: 11198866
    Abstract: Methods and systems for sample preparation techniques that allow amplification (e.g., whole genome amplification) and sequencing of chromatin accessible regions of single cells are provided. The methods and systems generally operate by forming or providing partitions (e.g., droplets) including a single biological particle and a single bead comprising a barcoded oligonucleotide. The preparation of barcoded next-generation sequencing libraries prepared from a single cell is facilitated by the transposon-mediated transposition and fragmentation of a target nucleic acid sequence. The methods and systems may be configured to allow the implementation of single-operation or multi-operation chemical and/or biochemical processing within the partitions.
    Type: Grant
    Filed: November 30, 2018
    Date of Patent: December 14, 2021
    Assignee: 10X GENOMICS, INC.
    Inventors: Zahra Kamila Belhocine, Geoffrey McDermott, Francesca Meschi, Xinying Zheng
  • Partitioning and processing of analytes and other species
    Patent number: 11193121
    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: October 25, 2018
    Date of Patent: December 7, 2021
    Assignee: 10X GENOMICS, INC.
    Inventors: Benjamin Hindson, Serge Saxonov, Kevin Ness, Paul Hardenbol, Christopher Hindson, Donald Masquelier, Mirna Jarosz, Michael Schnall-Levin
  • Methods and systems for droplet-based single cell barcoding
    Patent number: 11193122
    Abstract: Methods and systems are provided for sample preparation techniques and sequencing of macromolecular constituents of cells and other biological materials.
    Type: Grant
    Filed: March 22, 2021
    Date of Patent: December 7, 2021
    Assignee: 10X GENOMICS, INC.
    Inventors: Zahra Kamila Belhocine, Rajiv Bharadwaj, Christopher Hindson, Michael Schnall-Levin, Bill Kengli Lin, Anthony Makarewicz, Pranav Patel, Andrew D. Price, Mohammad Rahimi Lenji, Tobias Daniel Wheeler, Yifeng Yin
  • Methods and systems for processing polynucleotides
    Patent number: 11180805
    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: October 29, 2020
    Date of Patent: November 23, 2021
    Assignee: 10X GENOMICS, INC
    Inventors: Michael Ybarra Lucero, Tarjei Sigurd Mikkelsen, Katherine Pfeiffer, Stephane Claude Boutet
  • METHOD OF DETECTING TARGET NUCLEIC ACID MOLECULES
    Publication number: 20210340618
    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: Application
    Filed: June 1, 2021
    Publication date: November 4, 2021
    Applicant: 10x Genomics, Inc.
    Inventors: Malte KÜHNEMUND, Toon VERHEYEN
  • Single cell analysis of transposase accessible chromatin
    Patent number: 11155810
    Abstract: Methods and systems for sample preparation techniques that allow amplification (e.g., whole genome amplification) and sequencing of chromatin accessible regions of single cells are provided. The methods and systems generally operate by forming or providing partitions (e.g., droplets) including a single biological particle and a single bead comprising a barcoded oligonucleotide. The preparation of barcoded next-generation sequencing libraries prepared from a single cell is facilitated by the transposon-mediated transposition and fragmentation of a target nucleic acid sequence. The methods and systems may be configured to allow the implementation of single-operation or multi-operation chemical and/or biochemical processing within the partitions.
    Type: Grant
    Filed: April 6, 2020
    Date of Patent: October 26, 2021
    Assignee: 10X GENOMICS, INC.
    Inventors: Zahra Kamila Belhocine, Geoffrey McDermott, Francesca Meschi, Xinying Zheng
  • Systems and methods for quality control in single cell processing
    Patent number: 11155881
    Abstract: Provided are systems and methods for analyzing a single cell application or experiment. A set of control beads may be introduced to a biological sample and subjected to the single cell application. The control beads may be configured to mimic analytes in the biological sample, such as a cell or other analyte, and comprise one or more known sequences. The one or more known sequences may be identified to analyze the single cell application.
    Type: Grant
    Filed: June 6, 2019
    Date of Patent: October 26, 2021
    Assignee: 10X GENOMICS, INC.
    Inventors: Zachary Bent, Paul Ryvkin, Jessica Michele Terry, Geoffrey McDermott, Meghan Leigh Flanders Frey
  • Instrument systems for integrated sample processing
    Patent number: 11135584
    Abstract: An integrated system for processing and preparing samples for analysis may include a microfluidic device including a plurality of parallel channel networks for partitioning the samples including various fluids, and connected to a plurality of inlet and outlet reservoirs, at least a portion of the fluids comprising reagents, a holder including a closeable lid hingedly coupled thereto, in which in a closed configuration, the lid secures the microfluidic device in the holder, and in an open configuration, the lid is a stand orienting the microfluidic device at a desired angle to facilitate recovery of partitions or droplets from the partitioned samples generated within the microfluidic device, and an instrument configured to receive the holder and apply a pressure differential between the plurality of inlet and outlet reservoirs to drive fluid movement within the channel networks.
    Type: Grant
    Filed: February 12, 2019
    Date of Patent: October 5, 2021
    Assignee: 10x Genomics, Inc.
    Inventors: Donald A. Masquelier, Benjamin Hindson, Kevin Ness, Rajiv Bharadwaj
  • Systems and methods for nucleic acid sequence assembly
    Patent number: 11133084
    Abstract: Determination of a nucleic acid sequence using sequence reads of the nucleic acid. The reads, in sets of reads, include a first portion for a subset of the nucleic acid and a common second portion identifying a reaction partition that formed the read, where the partition has the subset of the nucleic acid in the form of a fragment. A set of k-mers is created for a read, with identifiers of the source reads for each k-mer are retained. The k-mers are used to determine whether to derive a contig sequence representative of the nucleic acid, where the contig comprises an origin node comprising a first set of overlapping k-mers and one of a first destination node comprising a second set of overlapping k-mers and a second destination node comprising a third set of overlapping k-mers. The sequence of the nucleic acid is assembled using at least the contig.
    Type: Grant
    Filed: November 2, 2017
    Date of Patent: September 28, 2021
    Assignee: 10X GENOMICS, INC.
    Inventors: Michael Schnall-Levin, Iain MacCallum
  • Methods and systems for macromolecule labeling
    Patent number: 11131664
    Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and analyte characterization from one or more cells. Such polynucleotide processing may be useful for a variety of applications, including generation of labeled macromolecules, including major mistocompatability complex (MHC) molecules, dextramers, etc. Labeled macromolecules may be generated using an in vitro transcription reaction. Labeled macromolecules may be generated in one or more partitions.
    Type: Grant
    Filed: April 4, 2019
    Date of Patent: September 28, 2021
    Assignee: 10X GENOMICS, INC.
    Inventors: Katherine Pfeiffer, Sarah Taylor, Michael Stubbington
  • METHOD FOR ISOLATING NUCLEI AND CELLS FROM TISSUES
    Publication number: 20210270703
    Abstract: A method of extracting and isolating fixed biological particles, such as fixed cells and/or fixed nuclei from snap-frozen biological tissue yields dramatically improved amounts of ligation products and an increase in targeted single cell RNA sequence data quality and sensitivity in subsequent RNA-templated ligation. The method preserves the integrity of the biological particles, such as cells and/or or nuclei from biological tissue samples during extraction and isolation by reducing the amount of cell degradation and RNA leakage associated with conventional methods.
    Type: Application
    Filed: February 26, 2021
    Publication date: September 2, 2021
    Applicant: 10X Genomics, Inc.
    Inventor: Jawad N. Abousoud
  • Microfluidic systems and methods of use
    Patent number: 11084036
    Abstract: Microfluidic channels networks and systems are provided. One network includes a first fluid channel having a first depth dimension; at least a second channel intersecting the first channel at a first intersection; at least a third channel in fluid communication with the first intersection, at least one of the first intersection and the third channel having a depth dimension that is greater than the first depth dimension. Also provided is a flow control system for directing fluids in the network. Systems are additionally provided for flowing disrupted particles into a droplet formation junction, whereby a portion of the disrupted particles or the contents thereof are encapsulated into one or more droplets. Further provided is a method for controlling filling of a microfluidic network by controlling passive valving microfluidic channel network features.
    Type: Grant
    Filed: November 5, 2018
    Date of Patent: August 10, 2021
    Assignee: 10X Genomics, Inc.
    Inventors: Rajiv Bharadwaj, Kevin Ness, Tobias Daniel Wheeler
  • CAPTURING OLIGONUCLEOTIDES IN SPATIAL TRANSCRIPTOMICS
    Publication number: 20210237022
    Abstract: Disclosed are extended and/or branched oligonucleotide capture probe assemblies for use in spatial transcriptomics systems, and methods for making the capture probe assemblies.
    Type: Application
    Filed: January 28, 2021
    Publication date: August 5, 2021
    Applicant: 10X Genomics, Inc.
    Inventor: Felice Alessio Bava
  • Systems, methods, and media for de novo assembly of whole genome sequence data
    Patent number: 11081208
    Abstract: Described are computer-implemented methods, systems, and media for de novo phased diploid assembly of nucleic acid sequence data generated from a nucleic acid sample of an individual utilizing nucleic acid tags to preserve long-range sequence context for the individual such that a subset of short-read sequence data derived from a common starting sequence shares a common tag. The phased diploid assembly is achieved without alignment to a reference sequence derived from organisms other than the individual. The methods, systems, and media described are computer-resource efficient, allowing scale-up.
    Type: Grant
    Filed: August 19, 2016
    Date of Patent: August 3, 2021
    Assignee: 10X GENOMICS, INC.
    Inventors: David Jaffe, Patrick Marks, Michael Schnall-Levin, Neil Weisenfeld