公开(公告)号：US11999945B2

公开(公告)日：2024-06-04

申请号：US17305230

申请日：2021-07-01

Applicant: Illumina, Inc.

Inventor： Steven Norberg ,  Dmitry K. Pokholok ,  Ramesh Ramji ,  Frank J. Steemers ,  Fan Zhang

IPC: C12N15/10 ,  B01L3/00 ,  C40B30/00 ,  C40B60/02 ,  C40B80/00

CPC classification number: C12N15/1006 ,  B01L3/502761 ,  C12N15/1065 ,  C40B30/00 ,  C40B60/02 ,  C40B80/00

Abstract: Systems, methods, and compositions provided herein relate to preparation of beads encapsulating biomolecules for performing sequential reactions on the biomolecules. Some embodiments include preparation of nucleic acid reactions within the bead, wherein the bead includes pores that allow diffusion of molecules into or out of the beads while retaining other molecules of interest.

公开(公告)号：US20240018584A1

公开(公告)日：2024-01-18

申请号：US18359299

申请日：2023-07-26

Applicant: ILLUMINA, INC.

Inventor： Lena Christiansen ,  Frank J. Steemers ,  Gary Schroth ,  Jerushah Thomas ,  Dmitry K. Pokholok

IPC: C12Q1/6874 ,  C12Q1/6858 ,  B01L3/00

CPC classification number: C12Q1/6874 ,  C12Q1/6858 ,  B01L3/502761 ,  C12Q1/6806

Abstract: Embodiments of systems, methods, and compositions provided herein relate to on bead tagmentation and droplet indexing. Some embodiments include performing co-assays on partitioned beads, including nucleic acid sequencing, indexed PCR, preparing nucleic acid libraries, determining methylation status, identifying genomic variants, or protein analysis.

公开(公告)号：US20190323003A1

公开(公告)日：2019-10-24

申请号：US16456763

申请日：2019-06-28

Applicant: ILLUMINA, INC.

Inventor： Ramesh Ramji ,  Frank J. Steemers ,  Lena Christiansen ,  Dmitry K. Pokholok ,  Fan Zhang

IPC: C12N15/10 ,  C12N9/12 ,  C12N9/22

Abstract: The invention relates to a system and methods for enhancing access to nuclear informational molecules, such as DNA, RNA, and proteins, by analytical biomolecules, such as transposome complexes, by treating nuclei with a nuclear permeability enhancer, and to methods of using nuclear membrane, cell membrane, and external compartmentalization approaches as contiguity preserving elements.

公开(公告)号：US12104281B2

公开(公告)日：2024-10-01

申请号：US17250848

申请日：2019-11-25

Applicant: ILLUMINA, INC.

Inventor： Frank J. Steemers ,  Fan Zhang ,  Dmitry K. Pokholok ,  Steven Norberg

IPC: C40B50/06 ,  C12Q1/6806 ,  C12Q1/6834

CPC classification number: C40B50/06 ,  C12Q1/6806 ,  C12Q1/6834 ,  C12Q2563/179

Abstract: Embodiments of systems, methods, and compositions provided herein relate to methods of simultaneously analyzing multiple analytes in a single sample using a single assay. Some embodiments relate to simultaneous analysis of DNA and RNA in a single sample, for example, to the simultaneous generation of DNA and RNA libraries.

公开(公告)号：US20200165650A1

公开(公告)日：2020-05-28

申请号：US16659475

申请日：2019-10-21

Applicant: Illumina, Inc.

Inventor： Gordon M. Cann ,  Jeffrey G. Mandell ,  Alex Aravanis ,  Steven Norberg ,  Dmitry K. Pokholok ,  Frank J. Steemers ,  Farnaz Absalan ,  Leila Bazargan

IPC: C12P19/34 ,  C12Q1/683 ,  C12Q1/6869 ,  C12Q1/6816 ,  C12N15/10

Abstract: A method for enriching a target nucleic acid comprising providing an endonuclease system having a crRNA or a derivative thereof, and a Cas protein or a variant thereof. The crRNA or the derivative thereof contains a target-specific nucleotide region substantially complementary to a region of the target nucleic acid; contacting the target nucleic acid with the endonuclease system to form a complex; and separating the complex and thereby enriching for the target nucleic acid.

公开(公告)号：US20180355348A1

公开(公告)日：2018-12-13

申请号：US16000505

申请日：2018-06-05

Applicant: OREGON HEALTH & SCIENCE UNIVERSITY ,  ILLUMINA, INC.

Inventor： Andrew C. Adey ,  Ryan Mulqueen ,  Frank J. Steemers ,  Dmitry K. Pokholok ,  Steven Norberg

IPC: C12N15/10

CPC classification number: C12N15/1065 ,  C12N15/1093 ,  C12Q1/6806 ,  C12Q1/6874 ,  C12Q2523/125 ,  C40B50/18 ,  C12Q2523/101 ,  C12Q2525/191 ,  C12Q2535/122 ,  C12Q2537/143 ,  C12Q2537/159 ,  C12Q2563/159 ,  C12Q2563/179

Abstract: Provided herein are methods for preparing sequencing libraries for determining the methylation status of nucleic acids from a plurality of single cells. The present methods combine split-and-pool combinatorial indexing and bisulfite treatment techniques to characterize the methylation profiles of large numbers of single cells quickly, accurately and inexpensively.

公开(公告)号：US20220333157A1

公开(公告)日：2022-10-20

申请号：US17663485

申请日：2022-05-16

Applicant: ILLUMINA, INC.

Inventor： Frank J. Steemers ,  Ramesh Ramji ,  Steven Norberg ,  Lena Christiansen ,  Dmitry K. Pokholok ,  Fan Zhang

IPC: C12Q1/6806 ,  A61K47/58 ,  A61K47/69 ,  C12M1/12 ,  C12N5/00 ,  C12N5/16

Abstract: Embodiments of systems, methods, and compositions provided herein relate to hollow beads encapsulating single cells. Some embodiments include performing multiple co-assays on a single cell encapsulated within a hollow bead, including nucleic acid sequencing, preparing nucleic acid libraries, determining methylation status, identifying genomic variants, or protein analysis.

公开(公告)号：US20220195507A1

公开(公告)日：2022-06-23

申请号：US17250846

申请日：2019-12-13

Applicant: ILLUMINA, INC.

Inventor： Frank J. Steemers ,  Dmitry K. Pokholok ,  Lena Christiansen

IPC: C12Q1/6848 ,  C12N15/10 ,  C12Q1/6874 ,  C12Q1/6876

Abstract: Embodiments of systems, methods, and compositions provided herein relate to assays for selectively controlling enzymatic reactions. Some embodiments relate to methods of inhibiting, reducing, or eliminating secondary DNA (such as mitochondrial DNA) sequencing reads from open chromatic sequencing, whole genome sequencing, or targeted sequencing.

公开(公告)号：US10457969B2

公开(公告)日：2019-10-29

申请号：US14804068

申请日：2015-07-20

Applicant: Illumina, Inc.

Inventor： Gordon M. Cann ,  Jeffrey G. Mandell ,  Alex Aravanis ,  Steven Norberg ,  Dmitry K. Pokholok ,  Frank J. Steemers ,  Farnaz Absalan ,  Leila Bazargan

IPC: C12P19/34 ,  C12N15/10 ,  C12Q1/6816 ,  C12Q1/683 ,  C12Q1/6869

Abstract: A method for enriching a target nucleic acid comprising providing an endonuclease system having a crRNA or a derivative thereof, and a Cas protein or a variant thereof. The crRNA or the derivative thereof contains a target-specific nucleotide region substantially complementary to a region of the target nucleic acid; contacting the target nucleic acid with the endonuclease system to form a complex; and separating the complex and thereby enriching for the target nucleic acid.

公开(公告)号：US12297565B2

公开(公告)日：2025-05-13

申请号：US17250846

申请日：2019-12-13

Applicant: ILLUMINA, INC.

Inventor： Frank J. Steemers ,  Dmitry K. Pokholok ,  Lena Christiansen

IPC: C40B50/06 ,  C12N15/10 ,  C12Q1/6848 ,  C12Q1/6874 ,  C12Q1/6876

Abstract: Embodiments of systems, methods, and compositions provided herein relate to assays for selectively controlling enzymatic reactions. Some embodiments relate to methods of inhibiting, reducing, or eliminating secondary DNA (such as mitochondrial DNA) sequencing reads from open chromatic sequencing, whole genome sequencing, or targeted sequencing.