公开(公告)号：US20250002996A1

公开(公告)日：2025-01-02

申请号：US18821083

申请日：2024-08-30

Applicant: 10x Genomics, Inc

Inventor： Felice Alessio BAVA

IPC: C12Q1/6874 ,  C12Q1/6876

Abstract: In some aspects, provided herein are methods for analyzing a nucleic acid comprising first and second regions of interest flanking an adaptor region, comprising hybridizing an anchor to the adaptor region, analyzing the first region of interest from one end of the anchor using probe ligation (e.g., sequencing-by-ligation), and binding a polymerase to the other end of the anchor and optionally incorporating a nucleotide and/or analog thereof into the anchor by the polymerase using the second region of interest or a probe bound thereto as a template. In some embodiments, the second region of interest is used as a template for sequencing-by-synthesis. In some embodiments, spatially resolved detections of analytes are performed at a cellular or subcellular resolution which involve correlating signals associated with analytes with specific spatial locations in a biological sample.

公开(公告)号：US20240376541A1

公开(公告)日：2024-11-14

申请号：US18774796

申请日：2024-07-16

Applicant: 10x Genomics, Inc.

Inventor： Felice Alessio BAVA ,  Eswar Prasad Ramachandran Iyer

IPC: C12Q1/6876 ,  C12Q1/6855

Abstract: The present disclosure relates in some aspects to 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 a set of three or more probe polynucleotides, for assessing target nucleic acids. In some aspects, the presence, amount, and/or identity of region of interest in a target nucleic acid is analyzed in situ. Also provided are polynucleotides, sets of polynucleotides, compositions, and kits for use in accordance with the methods.

公开(公告)号：US20240175083A1

公开(公告)日：2024-05-30

申请号：US18501746

申请日：2023-11-03

Applicant: 10x Genomics, Inc.

Inventor： Felice Alessio BAVA ,  Peter SMIBERT

IPC: C12Q1/6841 ,  C12Q1/682

CPC classification number: C12Q1/6841 ,  C12Q1/682

Abstract: In some aspects, the present disclosure relates to methods, compositions and kits for analyzing a biological sample using a hybridization-based polymerization reaction (HPR). In some aspects, a target nucleic acid molecule is detected via an HPR such as hybridization chain reaction (HCR). In some aspects, the HPR is initiated and terminated by an initiator sequence and terminator sequence, respectively, and the initiator sequence and terminator sequence are associated with the same target nucleic acid molecule.

公开(公告)号：US20240060119A1

公开(公告)日：2024-02-22

申请号：US18361069

申请日：2023-07-28

Applicant: 10x Genomics, Inc.

Inventor： Felice Alessio BAVA

IPC: C12Q1/682 ,  C12Q1/6841

CPC classification number: C12Q1/682 ,  C12Q1/6841

Abstract: The present disclosure in some aspects relates to methods and compositions for improved detection and quantification of one or more analytes present in a biological sample. In some aspects, the methods and compositions provided herein address issues associated with the heterogeneity of rolling circle amplification (RCA) products during in situ analyses. In some aspects, the methods and compositions disclosed herein provide more homogenous RCA products for improved sample imaging.

公开(公告)号：US20240026426A1

公开(公告)日：2024-01-25

申请号：US18356933

申请日：2023-07-21

Applicant: 10x Genomics, Inc.

Inventor： Felice Alessio BAVA

IPC: C12Q1/6837 ,  C12Q1/6844

CPC classification number: C12Q1/6837 ,  C12Q1/6844 ,  C12Q2600/166

Abstract: In some aspects, the present disclosure relates to methods for reducing the detection of false positive events during analysis of a biological sample. In some aspects, the method comprises use of a decoy oligonucleotide that can hybridize to a probe or to a target nucleic acid. The methods herein have particular applicability in reducing the detection of false positive events and in combining hybridization and ligation reactions into a single step. Also provided are kits comprising probes for use in such methods.

公开(公告)号：US20230324421A1

公开(公告)日：2023-10-12

申请号：US18132115

申请日：2023-04-07

Applicant: 10x Genomics, Inc.

Inventor： Yiran ZHANG ,  Felice Alessio BAVA ,  Rhyan Blaine DOCKTER ,  Rajiv BHARADWAJ

IPC: G01N35/00 ,  B01L3/00

CPC classification number: G01N35/00029 ,  B01L3/502715 ,  G01N2035/00168 ,  B01L2200/0689 ,  B01L2200/025 ,  B01L2300/0627 ,  B01L2200/16

Abstract: Disclosed herein are systems for receiving a biological sample for analysis and methods for preparing and/or analyzing a biological sample. In various embodiments, a system includes a first layer comprising a first region configured to receive a sample, a gasket disposed on the first layer such that the gasket surrounds the first region, and a housing layer. The first layer is disposed between the gasket and the housing layer. The system further includes a clamp configured to apply a force on the gasket to form a liquid tight seal against the first layer.

公开(公告)号：US20230183787A1

公开(公告)日：2023-06-15

申请号：US18079681

申请日：2022-12-12

Applicant: 10x Genomics, Inc.

Inventor： Felice Alessio BAVA ,  Toon VERHEYEN

IPC: C12Q1/6841 ,  C12Q1/682

CPC classification number: C12Q1/6841 ,  C12Q1/682

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.

公开(公告)号：US20210262018A1

公开(公告)日：2021-08-26

申请号：US17180325

申请日：2021-02-19

Applicant: 10x Genomics, Inc.

Inventor： Felice Alessio BAVA ,  Zachary BENT

IPC: C12Q1/6837 ,  C12Q1/6844

Abstract: In some embodiments, provided herein is an integrated assay of a biological sample comprising an in situ assay module and a spatial assay module. The in situ assay comprises analyzing binding between nucleic acid probes and a first analyte at a spatial location of the biological sample. In some embodiments, the method further comprises providing conditions to allow spatially barcoded capture agents to capture a second analyte for analysis in the spatial assay module.