公开(公告)号：US20220195505A1

公开(公告)日：2022-06-23

申请号：US17693116

申请日：2022-03-11

Applicant: Spatial Transcriptomics AB ,  Illumina, Inc.

Inventor： Jonas Frisen ,  Patrik Stahl ,  Joakim Lundeberg ,  Gordon M. Cann ,  Leila Bazargan ,  Alex Aravanis

IPC: C12Q1/6834 ,  C12Q1/6841 ,  C12Q1/6874 ,  C12N15/10 ,  C12Q1/6876

Abstract: A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.

公开(公告)号：US20220002791A1

公开(公告)日：2022-01-06

申请号：US17479718

申请日：2021-09-20

Applicant: Spatial Transcriptomics AB ,  Illumina, Inc.

Inventor： Jonas Frisen ,  Patrik Stahl ,  Joakim Lundeberg ,  Gordon M. Cann ,  Leila Bazargan ,  Alex Aravanis

IPC: C12Q1/6834 ,  C12Q1/6841 ,  C12Q1/6874 ,  C12N15/10 ,  C12Q1/6876

Abstract: A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.

公开(公告)号：US20210292748A1

公开(公告)日：2021-09-23

申请号：US17237652

申请日：2021-04-22

Applicant: Spatial Transcriptomics AB ,  Illumina, Inc.

Inventor： Jonas Frisen ,  Patrik Stahl ,  Joakim Lundeberg ,  Gordon M. Cann ,  Leila Bazargan ,  Alex Aravanis

IPC: C12N15/10

Abstract: A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.

公开(公告)号：US20140066318A1

公开(公告)日：2014-03-06

申请号：US14111482

申请日：2012-03-13

Applicant: Jonas Frisen ,  Patrik Ståhl ,  Joakim Lundeberg

Inventor： Jonas Frisen ,  Patrik Ståhl ,  Joakim Lundeberg

IPC: C12Q1/68

Abstract: The present invention relates to methods and products for the localized or spatial detection of nucleic acid in a tissue sample and in particular to a method for localized detection of nucleic acid in a tissue sample comprising: (a) providing an array comprising a substrate on which multiple species of capture probes are directly or indirectly immobilized such that each species occupies a distinct position on the array and is oriented to have a free 3′ end to enable said probe to function as a primer for a primer extension or ligation reaction, wherein each species of said capture probe comprises a nucleic acid molecule with 5′ to 3′: (i) a positional domain that corresponds to the position of the capture probe on the array, and (ii) a capture domain; (b) contacting said array with a tissue sample such that the position of a capture probe on the array may be correlated with a position in the tissue sample and allowing nucleic acid of the tissue sample to hybridize to the capture domain in said capture probes; (c) generating DNA molecules from the captured nucleic acid molecules using said capture probes as extension or ligation primers, wherein said extended or ligated DNA molecules are tagged by virtue of the positional domain; (d) optionally generating a complementary strand of said tagged DNA and/or optionally amplifying said tagged DNA; (e) releasing at least part of the tagged DNA molecules and/or their complements or amplicons from the surface of the array, wherein said part includes the positional domain or a complement thereof; and (f) directly or indirectly analyzing the sequence of the released DNA molecules.

Abstract translation: 本发明涉及用于组织样本中核酸的局部或空间检测的方法和产品，特别涉及组织样品中核酸的局部检测方法，包括：（a）提供包含基质的阵列， 直接或间接固定多种捕获探针，使得每个物种在阵列上占据不同的位置并且被定向为具有游离的3'末端以使得所述探针能够用作引物延伸或连接反应的引物，其中每个 所述捕获探针的种类包括具有5'至3'的核酸分子：（i）对应于阵列上的捕获探针的位置的位置结构域，和（ii）捕获结构域; （b）使所述阵列与组织样品接触，使得阵列上的捕获探针的位置可与组织样品中的位置相关，并允许组织样品的核酸与所述捕获探针中的捕获结构域杂交; （c）使用所述捕获探针作为延伸或连接引物从捕获的核酸分子产生DNA分子，其中所述延伸或连接的DNA分子由于位置结构域而被标记; （d）任选地产生所述标记的DNA的互补链和/或任选地扩增所述标记的DNA; （e）从阵列的表面释放标记的DNA分子和/或其补体或扩增子的至少一部分，其中所述部分包括位置结构域或其互补体; 和（f）直接或间接分析释放的DNA分子的序列。

公开(公告)号：US20230304078A1

公开(公告)日：2023-09-28

申请号：US18314437

申请日：2023-05-09

Applicant: Spatial Transcriptomics AB ,  Illumina, Inc.

Inventor： Jonas Frisen ,  Patrik Stahl ,  Joakim Lundeberg ,  Gordon M. Cann ,  Leila Bazargan ,  Alex Aravanis

IPC: C12Q1/6834 ,  C12Q1/6841 ,  C12Q1/6874 ,  C12N15/10 ,  C12Q1/6876

CPC classification number: C12Q1/6834 ,  C12Q1/6841 ,  C12Q1/6874 ,  C12N15/1065 ,  C12Q1/6876

Abstract: A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.

公开(公告)号：US11739372B2

公开(公告)日：2023-08-29

申请号：US18166853

申请日：2023-02-09

Applicant: Spatial Transcriptomics AB ,  Illumina, Inc.

Inventor： Jonas Frisen ,  Patrik Stahl ,  Joakim Lundeberg ,  Gordon M. Cann ,  Leila Bazargan ,  Alex Aravanis

IPC: C12Q1/6834 ,  C12Q1/6841 ,  C12Q1/6874 ,  C12Q1/6876 ,  C12N15/10

CPC classification number: C12Q1/6834 ,  C12N15/1065 ,  C12Q1/6841 ,  C12Q1/6874 ,  C12Q1/6876 ,  C12Q1/6841 ,  C12Q2525/131 ,  C12Q2525/173 ,  C12Q2525/179 ,  C12Q2535/122 ,  C12Q2563/149 ,  C12Q2565/515 ,  C12Q1/6874 ,  C12Q2525/131 ,  C12Q2525/173 ,  C12Q2525/179 ,  C12Q2535/122 ,  C12Q2543/10 ,  C12Q2563/149 ,  C12Q2565/515

Abstract: A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.

公开(公告)号：US20220298560A1

公开(公告)日：2022-09-22

申请号：US17834474

申请日：2022-06-07

Applicant: Spatial Transcriptomics AB ,  Illumina, Inc.

Inventor： Jonas Frisen ,  Patrik Stahl ,  Joakim Lundeberg ,  Gordon M. Cann ,  Leila Bazargan ,  Alex Aravanis

IPC: C12Q1/6834 ,  C12Q1/6876 ,  C12N15/10 ,  C12Q1/6841 ,  C12Q1/6874

Abstract: A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.

公开(公告)号：US11299774B2

公开(公告)日：2022-04-12

申请号：US17479718

申请日：2021-09-20

Applicant: Spatial Transcriptomics AB ,  Illumina, Inc.

Inventor： Jonas Frisen ,  Patrik Stahl ,  Joakim Lundeberg ,  Gordon M. Cann ,  Leila Bazargan ,  Alex Aravanis

IPC: C12Q1/6834 ,  C12Q1/6841 ,  C12Q1/6874 ,  C12Q1/6876 ,  C12N15/10

Abstract: A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.

公开(公告)号：US20210292822A1

公开(公告)日：2021-09-23

申请号：US17237670

申请日：2021-04-22

Applicant: Spatial Transcriptomics AB ,  Illumina, Inc.

Inventor： Jonas Frisen ,  Patrik Stahl ,  Joakim Lundeberg ,  Gordon M. Cann ,  Leila Bazargan ,  Alex Aravanis

IPC: C12Q1/6834 ,  C12Q1/6841 ,  C12Q1/6874 ,  C12Q1/6876

Abstract: A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.

公开(公告)号：US20210223227A1

公开(公告)日：2021-07-22

申请号：US17150997

申请日：2021-01-15

Applicant: Spatial Transcriptomics AB

Inventor： Marlon Stoeckius

IPC: G01N33/487 ,  G01N27/30 ,  G01N27/404

Abstract: An electrophoretic system is provided for analyte capture from a biological sample. The electrophoretic system can be used to permeabilize the sample to allow analytes to be released from the sample. For example, the sample can be contacted with capture probes attached to a substrate, and an electric field created by the electrophoretic system can cause analytes to be released from the cell, and effectively migrate toward and bind to the capture probes attached to the substrate.