Abstract: A recombinant ligase composition including a recombinantly-produced ligase isolated from Acanthocystis turfacea chlorella virus 1 (ATCV-1) fused to at least one polynucleotide-binding polypeptide is provided. Compositions containing the recombinant ligase composition, vectors encoding the recombinant ligase composition, and methods of making and using the recombinant ligase composition are also provided.
Type:
Application
Filed:
October 5, 2023
Publication date:
May 9, 2024
Applicant:
10x Genomics, Inc.
Inventors:
Shankar SHASTRY, Javelin C. CHI, Paul Eugene LUND
Abstract: A method for maintaining focus of an optical system on a target surface is provided. The method includes directing at least one beam of light through an objective lens to a sample, wherein the at least one beam of light is associated with at least two effective numerical apertures and receiving at least one reflected beam at the objective lens. The at least one reflected beam is associated with the at least two effective numerical apertures. The method also includes determining at least one image based on the at least one reflected beam, determining a baseline of a feature for each of the one or more objects, and when the feature differs from the baseline, adjusting a working distance between the objective lens and the sample.
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 6, 2023
Date of Patent:
April 30, 2024
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
Abstract: Provided herein are methods of identifying a location of an RNA in a sample that include: (a) contacting the sample with an array comprising capture probes, where a capture probe comprises a capture domain and a spatial barcode; (b) releasing the RNA from the sample; (c) extending a 3? end of the capture probe using the capture domain-bound RNA as a template; (d) generating nick(s) in the extended capture probe-hybridized RNA and performing random-primed DNA synthesis; (e) performing end repair on the second strand DNA molecule; (f) adding a single adenosine nucleotide to the 3? end of the extended capture probe; (g) ligating a double-stranded sequencing adaptor to the double-stranded DNA product; and (h) determining all or a part of the sequence of the RNA, and the sequence of the spatial barcode, or complements thereof, and using the determined sequences to identify the location of the RNA in the sample.
Abstract: Provided herein are systems and methods for processing biomolecules (e.g., nucleic acid molecules, proteins) from a sample. A method for processing biomolecules may comprise hybridizing a probe molecule to a target region of a nucleic acid molecule (e.g., a ribonucleic acid (RNA) molecule) and barcoding the probe-nucleic acid molecule complex or derivatives thereof. Such a method can comprise performing a nucleic acid reaction, e.g., extension, denaturation, and amplification. A method for processing a sample may comprise hybridizing probes to (i) target regions of a nucleic acid molecule (e.g., RNA molecule) and (ii) a reporter oligonucleotide of a feature binding group, and barcoding the probe-associated molecules. One or more processes of the methods described herein may be performed within a partition, such as a droplet or well.
Type:
Grant
Filed:
August 22, 2023
Date of Patent:
April 9, 2024
Assignee:
10X GENOMICS, INC.
Inventors:
Katherine Pfeiffer, Andrew Scott Kohlway, Andrew John Hill, Paul Eugene Lund
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.
Type:
Grant
Filed:
June 17, 2019
Date of Patent:
April 9, 2024
Assignee:
10X GENOMICS, INC.
Inventors:
Alexander Y. Wong, Jeffrey Mellen, Kevin J. Wu, Paul Ryvkin, Preyas Shah, Patrick Marks, Niranjan Srinivas
Abstract: Systems, and their methods of use, for sorting or separating magnetic particles are provided. A system having a magnetic module with features that mate with voids in a flow module exerts a magnetic field on magnetic particles to separate particles.
Abstract: A method for identifying framework regions and complementarity-determining regions in an amino acid sequence. The amino acid sequence is received. A plurality of candidate start positions is identified within the amino acid sequence for a start position for a selected region of interest. A score is generated for each candidate start position of the plurality of candidate start positions via analysis of a motif window that begins at each candidate start position. The start position for the selected region of interest is identified based on a candidate start position of the plurality of candidate start positions having a highest score.
Type:
Application
Filed:
August 23, 2023
Publication date:
March 21, 2024
Applicant:
10X GENOMICS, INC.
Inventors:
David Benjamin JAFFE, Wyatt James MCDONNELL
Abstract: The present disclosure relates to materials and methods for spatially analyzing nucleic acids fragmented with a transposase enzyme in a biological sample.
Type:
Application
Filed:
January 7, 2022
Publication date:
March 21, 2024
Applicant:
10x Genomics, Inc.
Inventors:
Patrik Stahl, Maja Marklund, Enric Llorens Bobadilla, Jonas Frisen
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.
Abstract: Provided herein are methods and systems for characterizing a nucleic acid molecule from a single cell. A method for characterizing a nucleic acid molecule from a single cell may comprise providing a partition (e.g., droplets or wells) comprising a single cell and a single bead. The single bead may comprise a nucleic acid barcode molecule. A nucleic acid molecule from the single cell and the nucleic acid barcode molecule may be used to generate a barcoded nucleic acid molecule for sequencing, which may be used to determine an epigenetic state or characteristic of the nucleic acid molecule as being associated with the single cell.
Type:
Grant
Filed:
June 6, 2019
Date of Patent:
March 19, 2024
Assignee:
10X GENOMICS, INC.
Inventors:
Kamila Belhocine, Michael Schnall-Levin, Andrew D. Price
Abstract: A sample holder includes a first member featuring a first retaining mechanism configured to retain a first substrate that includes a sample, a second member featuring a second retaining mechanism configured to retain a second substrate that includes a reagent medium, and an alignment mechanism connected to at least one of the first and second members, and configured to align the first and second members such that the sample contacts at least a portion of the reagent medium when the first and second members are aligned.
Type:
Grant
Filed:
February 27, 2023
Date of Patent:
March 19, 2024
Assignee:
10x Genomics, Inc.
Inventors:
Augusto Manuel Tentori, Rajiv Bharadwaj, Felice Alessio Bava
Abstract: This disclosure relates to compositions and methods for three-dimensional spatial profiling of analytes in a biological sample. The methods include use of a hydrogel comprising one or more polymers that include a phenol moiety, an azide moiety, or an alkyne moiety.
Abstract: A method of analyzing single biological particles, such as cells or nuclei, that maintains the single biological particles in a state of relative isolation during decrosslinking and subsequent processing is provided. In the case of cells, the method prevents cellular analytes from each individual cell from leaving the cell site and diffusing toward adjacent cells, while permitting transmission of a decrosslinking agent, followed by processing of the cellular analytes from the individual cells by barcoding and/or imaging of the cellular analytes.
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 16, 2023
Date of Patent:
March 12, 2024
Assignee:
10x Genomics, Inc.
Inventors:
Yifeng Yin, Michael Schnall-Levin, Eswar Prasad Ramachandran Iyer
Abstract: Provided in some aspects are methods for light-controlled in situ surface patterning of a substrate comprising a step of blocking or ablating oligonucleotide molecules in a boundary region separating a plurality of spot regions, and attaching oligonucleotides to oligonucleotide molecules in a first one or more of the spot regions.
Type:
Application
Filed:
June 28, 2023
Publication date:
March 7, 2024
Applicant:
10x Genomics, Inc.
Inventors:
David Michael PATTERSON, Steven William SHORT, Dieter WILK, Pingwei ZHUANG, Solongo Batjargal ZIRALDO