公开(公告)号：US20250034624A1

公开(公告)日：2025-01-30

申请号：US18763973

申请日：2024-07-03

Applicant: 10x Genomics, Inc.

Inventor： Felice Alessio BAVA

IPC: C12Q1/6827 ,  C12Q1/6841 ,  C12Q1/6853 ,  C12Q1/6876

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 polynucleotides, including one or more polynucleotides (e.g., a detection padlock probe) for detecting a region of interest and one or more polynucleotides (e.g., a control padlock probe) as an internal control, for analyzing target nucleic acids. In some aspects, the presence, amount, and/or identity of a 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：US20240167081A1

公开(公告)日：2024-05-23

申请号：US18503949

申请日：2023-11-07

Applicant: 10x Genomics,Inc.

Inventor： Felice Alessio BAVA ,  Cheyenne CHRISTOPHERSON ,  Justin COSTA ,  Shalini GOHIL ,  Christina GALONSKA ,  Monica NAGENDRAN

IPC: C12Q1/682 ,  C12Q1/6841 ,  C12Q1/6844 ,  C12Q1/6876 ,  G01N1/30

CPC classification number: C12Q1/682 ,  C12Q1/6841 ,  C12Q1/6844 ,  C12Q1/6876 ,  G01N1/30

Abstract: The present disclosure relates in some aspects to methods and compositions for immobilization of nucleic acids for in situ detection in a biological sample or a matrix embedding the biological sample.

公开(公告)号：US20210238662A1

公开(公告)日：2021-08-05

申请号：US17165808

申请日：2021-02-02

Applicant: 10x Genomics, Inc.

Inventor： Felice Alessio BAVA ,  Patrick J. MARKS

IPC: C12Q1/6832 ,  C12Q1/6841

Abstract: Provided herein are methods for analyzing a target nucleic acid, comprising contacting a target nucleic acid with a first polynucleotide and a second polynucleotide, and optionally one or more other polynucelotides such as a splint and/or a primer, to form a hybridization complex. In some embodiments, the first polynucleotide and the second polynucleotide are ligated to form a circular polynucleotide hybridized to the target nucleic acid, e.g., using DNA-templated ligation reaction(s). The circular polynucleotide and/or a product thereof (e.g., an RCA product) can be analyzed to analyze the target nucleic acid or a sequence thereof.

公开(公告)号：US20250137040A1

公开(公告)日：2025-05-01

申请号：US18943775

申请日：2024-11-11

Applicant: 10x Genomics, Inc.

Inventor： Felice Alessio BAVA ,  Zachary W. 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.

公开(公告)号：US20220282316A1

公开(公告)日：2022-09-08

申请号：US17685033

申请日：2022-03-02

Applicant: 10x Genomics, Inc.

Inventor： Felice Alessio BAVA

IPC: C12Q1/6837 ,  C12Q1/6874

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 oligonucleotides, for example a set of two or more oligonucleotides, wherein one or more oligonucleotides comprises modified nucleotides, for assessing target nucleic acids. In some aspects, the presence, amount, and/or identity of a target nucleic acid is analyzed in situ. Also provided are oligonucleotides, sets of oligonucleotides, compositions, and kits for use in accordance with the methods.

公开(公告)号：US20210277460A1

公开(公告)日：2021-09-09

申请号：US17192746

申请日：2021-03-04

Applicant: 10x Genomics, Inc.

Inventor： Felice Alessio BAVA

IPC: C12Q1/6869 ,  C12Q1/6832

Abstract: In some embodiments described herein are methods for three-dimensional analysis of a biological sample, comprising migrating a population of spatial probes into the biological sample in each of three dimensions, wherein each spatial probe comprises a targeting domain and a migration domain. Also provided are kits and compositions for use according to any of the methods described herein.

公开(公告)号：US20240331348A1

公开(公告)日：2024-10-03

申请号：US18737862

申请日：2024-06-07

Applicant: 10x Genomics, Inc.

Inventor： Felice Alessio BAVA ,  David Hoffman ,  Elijah Roberts

IPC: G06V10/60 ,  G06T3/40 ,  G06T7/70 ,  G06V10/10 ,  G06V20/69

CPC classification number: G06V10/60 ,  G06T3/40 ,  G06T7/70 ,  G06V10/19 ,  G06V20/693

Abstract: Methods and systems for performing multi-resolution in situ decoding are described. The method may comprise, for example, acquiring at least one first image of a biological sample at a first optical resolution; identifying locations for a plurality of target analytes based on the at least one first image; acquiring at least one second image of the biological sample at a second optical resolution in at least one decoding cycle of a plurality of decoding cycles used for in situ decoding of the target analytes; and extracting signal intensity data for signals associated with all or a portion of the target analytes from the at least one second image based on the locations for the target analytes identified in the at least one first image. In some instances, the method may further comprise using the signal intensity data extracted from the at least one second image to decode the target analytes.

公开(公告)号：US20230416821A1

公开(公告)日：2023-12-28

申请号：US18300814

申请日：2023-04-14

Applicant: 10x Genomics, Inc.

Inventor： Felice Alessio BAVA ,  Marco Mignardi

IPC: C12Q1/6881 ,  C12Q1/6841

CPC classification number: C12Q1/6881 ,  C12Q1/6841

Abstract: In some aspects disclosed herein are methods and compositions for detecting an analyte such as a target nucleic acid in a biological sample, said method comprising generating and analyzing a detectable signal associated with the target nucleic acid and a separate signal associated with a region of interest in the target nucleic acid.

公开(公告)号：US20230287478A1

公开(公告)日：2023-09-14

申请号：US18120024

申请日：2023-03-10

Applicant: 10x Genomics, Inc.

Inventor： Felice Alessio BAVA

IPC: C12Q1/6816 ,  C12Q1/6844 ,  C12Q1/6874

CPC classification number: C12Q1/6816 ,  C12Q1/6844 ,  C12Q1/6874

Abstract: The present disclosure relates in some aspects to methods, probes, and kits for detection of a target analyte in a sample. In some embodiments, disclosed herein are methods in which a biological sample is contacted with a pre-formed detectable probe comprising a concatemeric region, e.g., a rolling circle amplification (RCA) product, comprising multiple copies of a unit sequence. Also disclosed herein are related probes and kits.

公开(公告)号：US20220282306A1

公开(公告)日：2022-09-08

申请号：US17683856

申请日：2022-03-01

Applicant: 10x Genomics, Inc.

Inventor： Felice Alessio BAVA

IPC: C12Q1/6816

Abstract: The present disclosure provides methods for detecting a nucleic acid molecule involving the use of a signal code sequence which corresponds to said nucleic acid molecule, comprising sequential hybridization of detectably labeled probes to allow detection of a signal code sequence. In particular, the present disclosure provides a method of sequential decoding comprising hybridization-directed quenching of detectable moieties that have already been imaged, allowing the newly added probe to be detected without the need to remove the previously imaged detectable moiety, thus providing an approach that reduces or eliminates the need for damaging probe stripping.