公开(公告)号：US20240117416A1

公开(公告)日：2024-04-11

申请号：US18274974

申请日：2022-01-28

申请人： Illumina, Inc. ,  Illumina Cambridge Limited

发明人： Yir-Shyuan Wu ,  Filiz Gorpe-Yasar ,  Tarun Kuman Khurana ,  Jonathan Mark Boutell

IPC分类号： C12Q1/6834 ,  C12Q1/6844 ,  C12Q1/6874

CPC分类号： C12Q1/6834 ,  C12Q1/6844 ,  C12Q1/6874

摘要： The disclosure relates to methods, compositions, and kits for improving seeding efficiency of flow cells with polynucleotides, and applications thereof, including for sequencing.

公开(公告)号：US11702695B2

公开(公告)日：2023-07-18

申请号：US17662124

申请日：2022-05-05

申请人： Illumina, Inc.

发明人： Yir-Shyuan Wu ,  Yan-You Lin ,  M. Shane Bowen ,  Cyril Delattre ,  Fabien Abeille ,  Tarun Khurana ,  Arnaud Rival ,  Poorya Sabounchi ,  Dajun Yuan ,  Maria Candelaria Rogert Bacigalupo

IPC分类号： B05D3/06 ,  G03F7/00 ,  G03F7/20 ,  C12Q1/6874 ,  C12Q1/6806

CPC分类号： C12Q1/6874 ,  B05D3/06 ,  C12Q1/6806 ,  G03F7/0002 ,  G03F7/20

摘要： Embodiments provided herewith are directed to self-assembled methods of preparing a patterned surface for sequencing applications including, for example, a patterned flow cell or a patterned surface for digital fluidic devices. The methods utilize photolithography to create a patterned surface with a plurality of microscale or nanoscale contours, separated by hydrophobic interstitial regions, without the need of oxygen plasma treatment during the photolithography process. In addition, the methods avoid the use of any chemical or mechanical polishing steps after the deposition of a gel material to the contours.

公开(公告)号：US20220331792A1

公开(公告)日：2022-10-20

申请号：US17729814

申请日：2022-04-26

申请人： ILLUMINA, INC.

发明人： 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分类号： B01L3/00 ,  C12N15/10

摘要： 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：US20220106588A1

公开(公告)日：2022-04-07

申请号：US17451771

申请日：2021-10-21

申请人： Illumina, Inc.

发明人： Yir-Shyuan Wu ,  Filiz Gorpe-Yasar ,  Tarun Kumar Khurana ,  Victoria Popic ,  Erich B. Jaeger ,  Mostafa Ronaghi

IPC分类号： C12N15/10 ,  C12Q1/6806 ,  B01L3/00 ,  B01L7/00 ,  C12Q1/6834

摘要： Systems, methods, and compositions provided herein relate to preparation of beads encapsulating long DNA fragments for high-throughput spatial indexing. Some embodiments include preparation of nucleic acid libraries within the bead, wherein the bead includes pores that allow diffusion of reagents while retaining genetic material.

公开(公告)号：US20220080415A1

公开(公告)日：2022-03-17

申请号：US17420048

申请日：2020-07-22

申请人： ILLUMINA, INC.

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

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

摘要： 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：US20200224267A1

公开(公告)日：2020-07-16

申请号：US16837463

申请日：2020-04-01

申请人： Illumina, Inc.

发明人： Robert C. Kain ,  Tarun Khurana ,  Kevin L. Gunderson ,  Yir-Shyuan Wu

IPC分类号： C12Q1/6874 ,  C12Q1/6825 ,  C12Q1/6837 ,  G01N21/64

摘要： A detection apparatus that includes (a) an array of responsive pads on a substrate surface; (b) an array of pixels, wherein each pixel in the array has a detection zone on the surface that includes a subset of at least two of the pads; and (c) an activation circuit to apply a force at a first and second pad in the subset, wherein the activation circuit is configured to apply a different force at the first pad compared to the second pad, and wherein the activation circuit has a switch to selectively alter the force at the first pad and the second pad.

公开(公告)号：US11697847B2

公开(公告)日：2023-07-11

申请号：US16837463

申请日：2020-04-01

申请人： Illumina, Inc.

发明人： Robert C. Kain ,  Tarun Khurana ,  Kevin L. Gunderson ,  Yir-Shyuan Wu

IPC分类号： G01N21/64 ,  C12Q1/6825 ,  C12Q1/6874 ,  C12Q1/6837

CPC分类号： C12Q1/6874 ,  C12Q1/6825 ,  C12Q1/6837 ,  G01N21/6454 ,  C12Q1/6825 ,  C12Q2563/103 ,  C12Q2563/113 ,  C12Q2563/179 ,  C12Q2565/101 ,  C12Q2565/101 ,  C12Q2565/607 ,  C12Q1/6837 ,  C12Q2563/103 ,  C12Q2563/113 ,  C12Q2563/179 ,  C12Q2565/101 ,  C12Q2565/101 ,  C12Q2565/607 ,  C12Q1/6874 ,  C12Q2563/103 ,  C12Q2563/113 ,  C12Q2563/179 ,  C12Q2565/101 ,  C12Q2565/101 ,  C12Q2565/607

摘要： A detection apparatus that includes (a) an array of responsive pads on a substrate surface; (b) an array of pixels, wherein each pixel in the array has a detection zone on the surface that includes a subset of at least two of the pads; and (c) an activation circuit to apply a force at a first and second pad in the subset, wherein the activation circuit is configured to apply a different force at the first pad compared to the second pad, and wherein the activation circuit has a switch to selectively alter the force at the first pad and the second pad.

公开(公告)号：US11649498B2

公开(公告)日：2023-05-16

申请号：US17720187

申请日：2022-04-13

申请人： ILLUMINA, INC.

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

IPC分类号： C12Q1/6874 ,  C12Q1/6813

CPC分类号： C12Q1/6874 ,  C12Q1/6813 ,  C12Q2565/514 ,  C12Q2600/156

摘要： 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

申请人： ILLUMINA, INC.

发明人： 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分类号： B01L3/00 ,  C12N15/10

摘要： 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

申请人： ILLUMINA, INC.

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

IPC分类号： C12Q1/6874 ,  C12Q1/6813

摘要： 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.