Illumina Corporation

Illumina Cambridge Limited

Whitehead Institute for Biomedical Research

Oregon Health & Science University

Dmitry K Pokholok

Frank J Steemers

Fan Zhang

Steven Norberg

Ramesh Ramji

Kevin L Gunderson

Lena Christiansen

Jian-Bing Fan

Fiona Kaper

Molly Min He

Niall Anthony Gormley

Richard A Young

Jeffrey G Mandell

Alex Aravanis

Amirali Kia

Gordon M Cann

Igor Yu Goryshin

Jason Richard Betley

Eric Hans Vermaas

Rigo Pantoja

Leila Bazargan

Natalie Morrell

Wouter Meuleman

Rosamond Jackson

Gary Schroth

Farnaz Absalan

Gareth Jenkins

Avgousta Ioannou

Andrew C Adey

Jacqueline Weir

Steven J Norberg

Weihua Chang

Megan Chu

Patrizia Iavicoli

Ryan Mulqueen

Jeffrey Brodin

Igor Goryshin

Jerushah Thomas

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.

Analysis system for orthogonal access to and tagging of biomolecules in cellular compartments

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.

Methods and means for preparing a library for sequencing

The present disclosure relates to systems and methods for the amplification of nucleic acids, including, but not limited to, the amplification of nucleic acid libraries and whole genome amplification.

Compositions and methods for the amplification of nucleic acids

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.

Analysis of multiple analytes using a single assay

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.

Modulating polymer beads for DNA processing

Embodiments provided herein relate to methods and compositions for preparing an immobilized library of barcoded DNA fragments of a target nucleic acid, identifying genomic variants, determining the contiguity information, phasing information, and methylation status of the target nucleic acid.

Contiguity preserving transposition

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.

Contiguity particle formation and methods of use

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.

Polynucleotide enrichment using CRISPR-Cas systems

The invention relates to improved methods of identifying the gene expression programs that are regulated by a signal transduction pathway. The invention also provides methods of identifying agents which modulate signal transduction pathway. The invention also provides improved methods of isolating DNA fragments to which a protein of interest is bound, and genome-wide location analysis methods employing these improved isolation methods.

Methods for mapping signal transduction pathways to gene expression programs

Growing community of inventors

San Diego, CA, United States of America

Dmitry K Pokholok