公开(公告)号：US11649498B2

公开(公告)日：2023-05-16

申请号：US17720187

申请日：2022-04-13

Applicant: ILLUMINA, INC.

Inventor： Tarun Kumar Khurana ,  Yir-Shyuan Wu ,  Xi-Jun Chen ,  Filiz Gorpe-Yasar ,  Yan-You Lin ,  Victoria Popic ,  Erich B. Jaeger ,  Mostafa Ronaghi

IPC: C12Q1/6874 ,  C12Q1/6813

CPC classification number: C12Q1/6874 ,  C12Q1/6813 ,  C12Q2565/514 ,  C12Q2600/156

Abstract: Implementations of a method for seeding sequence libraries on a surface of a sequencing flow cell that allow for spatial segregation of the libraries on the surface are provided. The spatial segregation can be used to index sequence reads from individual sequencing libraries to increase efficiency of subsequent data analysis. In some examples, hydrogel beads containing encapsulated sequencing libraries are captured on a sequencing flow cell and degraded in the presence of a liquid diffusion barrier to allow for the spatial segregation and seeding of the sequencing libraries on the surface of the flow cell. Additionally, examples of systems, methods and compositions are provided relating to flow cell devices configured for nucleic acid library preparation and single cell sequencing. Some examples include flow cell devices having a hydrogel with genetic material disposed therein, and which is retained within the hydrogel during nucleic acid processing.

公开(公告)号：US20220410146A1

公开(公告)日：2022-12-29

申请号：US17898155

申请日：2022-08-29

Applicant: ILLUMINA, INC.

Inventor： Tarun Kumar Khurana ,  Arnaud Rival ,  Lewis J. Kraft ,  Steven Barnard ,  M. Shane Bowen ,  Xi-Jun Chen ,  Yir-Shyuan Wu ,  Jeffrey S. Fisher ,  Dajun Yuan

IPC: B01L3/00 ,  C12N15/10

Abstract: An example of a flow cell includes a substrate, which includes nano-depressions defined in a surface of the substrate, and interstitial regions separating the nano-depressions. A hydrophobic material layer has a surface that is at least substantially co-planar with the interstitial regions and is positioned to define a hydrophobic barrier around respective sub-sets of the nano-depressions.

公开(公告)号：US20220243269A1

公开(公告)日：2022-08-04

申请号：US17720187

申请日：2022-04-13

Applicant: ILLUMINA, INC.

Inventor： Tarun Kumar Khurana ,  Yir-Shyuan Wu ,  Xi-Jun Chen ,  Filiz Gorpe-Yasar ,  Yan-You Lin ,  Victoria Popic ,  Erich B. Jaeger ,  Mostafa Ronaghi

IPC: C12Q1/6874 ,  C12Q1/6813

Abstract: Implementations of a method for seeding sequence libraries on a surface of a sequencing flow cell that allow for spatial segregation of the libraries on the surface are provided. The spatial segregation can be used to index sequence reads from individual sequencing libraries to increase efficiency of subsequent data analysis. In some examples, hydrogel beads containing encapsulated sequencing libraries are captured on a sequencing flow cell and degraded in the presence of a liquid diffusion barrier to allow for the spatial segregation and seeding of the sequencing libraries on the surface of the flow cell. Additionally, examples of systems, methods and compositions are provided relating to flow cell devices configured for nucleic acid library preparation and single cell sequencing. Some examples include flow cell devices having a hydrogel with genetic material disposed therein, and which is retained within the hydrogel during nucleic acid processing.

公开(公告)号：US20240060954A1

公开(公告)日：2024-02-22

申请号：US18385442

申请日：2023-10-31

Applicant: ILLUMINA, INC.

Inventor： Tarun Khurana ,  Ali Agah ,  Aathavan Karunakaran ,  Xi-Jun Chen

IPC: G01N33/483 ,  G01N33/50 ,  G01N33/53

CPC classification number: G01N33/4836 ,  G01N33/5047 ,  G01N33/5308 ,  A61K39/12

Abstract: Methods are used for obtaining, cataloguing, and/or storing data derived from a biological source using a flow cell body, electrodes, and an imaging assembly. The data may include DNA and/or RNA obtained from a biological source, such as from the cells of an organism. The methods may be used to obtain, catalog, and/or store data such as DNA or RNA sequence from a pathogen such as a virus and/or a bacteria, human health data over time, and immune system information from an individual. The data obtained using the disclosed methods may be used for a variety of different purposes, including the manufacture of vaccine compositions, and for restoring the immune system of an individual who has undergone an immune system depleting event. The methods may be used for storage of biological cells, which may be used for the screening of compounds, such as small molecules with potential for therapeutic indications.

公开(公告)号：US11518993B2

公开(公告)日：2022-12-06

申请号：US16494902

申请日：2018-03-16

Applicant: Illumina, Inc.

Inventor： Xi-Jun Chen ,  Tarun Khurana

IPC: C12N15/10

Abstract: Systems, methods and compositions provided herein relate to the preparation of nucleic acid libraries. Some embodiments include the preparation of nucleic acid libraries by ligation of single-stranded nucleic acids.

公开(公告)号：US20220331792A1

公开(公告)日：2022-10-20

申请号：US17729814

申请日：2022-04-26

Applicant: ILLUMINA, INC.

Inventor： Tarun Kumar Khurana ,  Arnaud Rival ,  Lewis J. Kraft ,  Steven Barnard ,  M. Shane Bowen ,  Xi-Jun Chen ,  Yir-Shyuan Wu ,  Jeffrey S. Fisher ,  Dajun Yuan

IPC: B01L3/00 ,  C12N15/10

Abstract: An example of a flow cell includes a substrate, which includes nano-depressions defined in a surface of the substrate, and interstitial regions separating the nano-depressions. A hydrophobic material layer has a surface that is at least substantially co-planar with the interstitial regions and is positioned to define a hydrophobic barrier around respective sub-sets of the nano-depressions.

公开(公告)号：US20220080415A1

公开(公告)日：2022-03-17

申请号：US17420048

申请日：2020-07-22

Applicant: ILLUMINA, INC.

Inventor： Yir-Shyuan Wu ,  Tarun Kumar Khurana ,  Yasaman Farshchi ,  Xi-Jun Chen ,  Bernard Hirschbein

IPC: B01L3/00 ,  C12Q1/6806 ,  C08J9/36 ,  C08F220/56

Abstract: An example of a flow cell includes a substrate and a cationic polymeric hydrogel on the substrate. The cationic polymeric hydrogel includes a cationic moiety that is i) integrated into a monomeric unit of an initial polymeric hydrogel or ii) attached to the monomeric unit of the initial polymeric hydrogel through a linker. The flow cell further includes an amplification primer attached to the cationic polymeric hydrogel.

公开(公告)号：US20250091042A1

公开(公告)日：2025-03-20

申请号：US18965657

申请日：2024-12-02

Applicant: ILLUMINA, INC.

Inventor： Lewis J. Kraft ,  Tarun Kumar Khurana ,  Yir-Shyuan Wu ,  Xi-Jun Chen ,  Arnaud Rival ,  Justin Fullerton ,  M. Shane Bowen ,  Hui Han ,  Jeffrey S. Fisher ,  Yasaman Farshchi ,  Mathieu Lessard-Viger

IPC: B01L3/00 ,  B01J19/00 ,  C08L37/00 ,  C12N15/10 ,  C40B40/08 ,  C40B50/18 ,  G01N21/05

Abstract: An example of a flow cell includes a substrate, a plurality of chambers defined on or in the substrate, and a plurality of depressions defined in the substrate and within a perimeter of each of the plurality of chambers. The depressions are separated by interstitial regions. Primers are attached within each of the plurality of depressions, and a capture site is located within each of the plurality of chambers.

公开(公告)号：US11819843B2

公开(公告)日：2023-11-21

申请号：US17729814

申请日：2022-04-26

Applicant: ILLUMINA, INC.

Inventor： Tarun Kumar Khurana ,  Arnaud Rival ,  Lewis J. Kraft ,  Steven Barnard ,  M. Shane Bowen ,  Xi-Jun Chen ,  Yir-Shyuan Wu ,  Jeffrey S. Fisher ,  Dajun Yuan

IPC: B01L3/00 ,  C12N15/10 ,  C08K5/54 ,  C08L37/00

CPC classification number: B01L3/5027 ,  B01L3/5085 ,  C12N15/1065 ,  B01L3/5088 ,  B01L2300/0896 ,  B01L2300/161 ,  B01L2300/165 ,  C08K5/5406 ,  C08L37/00

Abstract: An example of a flow cell includes a substrate, which includes nano-depressions defined in a surface of the substrate, and interstitial regions separating the nano-depressions. A hydrophobic material layer has a surface that is at least substantially co-planar with the interstitial regions and is positioned to define a hydrophobic barrier around respective sub-sets of the nano-depressions.

公开(公告)号：US20230220462A1

公开(公告)日：2023-07-13

申请号：US18180622

申请日：2023-03-08

Applicant: ILLUMINA, INC.

Inventor： Tarun Kumar Khurana ,  Yir-Shyuan Wu ,  Xi-Jun Chen ,  Filiz Gorpe-Yasar ,  Yan-You Lin ,  Victoria Popic ,  Erich B. Jaeger ,  Mostafa Ronaghi

IPC: C12Q1/6874 ,  C12Q1/6813

CPC classification number: C12Q1/6874 ,  C12Q1/6813 ,  C12Q2600/156 ,  C12Q2565/514

Abstract: Implementations of a method for seeding sequence libraries on a surface of a sequencing flow cell that allow for spatial segregation of the libraries on the surface are provided. The spatial segregation can be used to index sequence reads from individual sequencing libraries to increase efficiency of subsequent data analysis. In some examples, hydrogel beads containing encapsulated sequencing libraries are captured on a sequencing flow cell and degraded in the presence of a liquid diffusion barrier to allow for the spatial segregation and seeding of the sequencing libraries on the surface of the flow cell. Additionally, examples of systems, methods and compositions are provided relating to flow cell devices configured for nucleic acid library preparation and single cell sequencing. Some examples include flow cell devices having a hydrogel with genetic material disposed therein, and which is retained within the hydrogel during nucleic acid processing.