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.
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.
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
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.
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.
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
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
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.
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.
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
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.
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.
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
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
Abstract: The present disclosure relates in some aspects to methods and compositions for analyzing a target nucleic acid, such as in situ detection of a region of interest in a polynucleotide in a cell or tissue sample. In some aspects, provided herein are circular probes (e.g., dumbbell probes) for analyzing a target nucleic acid, as well as methods comprising an enzymatic treatment to de-circularize unbound or non-specifically bound circular probes. Circular probes specifically bound to target nucleic acids remain intact during and after the enzymatic treatment and can be detected, e.g., via rolling circle amplification (RCA) of the circular probes and detection of the RCA products.
Abstract: Provided herein are methods and systems for establishing the presence of a sequence element in nucleic acid molecules. The sequence element may comprise a fused gene, a reporter gene, or another useful sequence for cell and tissue engineering, such as those used for labeling cells, identifying successfully transfected or transduced cells, etc. A method provided herein may additionally allow for barcoding of nucleic acid molecules and analysis of libraries of barcoded nucleic acid molecules.
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:
Grant
Filed:
March 25, 2021
Date of Patent:
May 16, 2023
Assignee:
10x Genomics, Inc.
Inventors:
Yifeng Yin, Eswar Prasad Ramachandran Iyer, Zachary Bent, Stefania Giacomello, Meghan L. F. Frey, Alexander Gagnon, Erik Leonard Henrik Borgstrom