10x Genomics, Inc.

Andrew D Price

Christopher Hindson

Michael Schnall-Levin

Katherine Pfeiffer

Rajiv Bharadwaj

Tarjei Sigurd Mikkelsen

Tobias Daniel Wheeler

Zahra Kamila Belhocine

Yifeng Yin

Mohammad Rahimi Lenji

Serge Saxonov

Zachary Bent

John R Stuelpnagel

Paul Hardenbol

Geoffrey McDermott

Paul Ryvkin

Jessica Michele Terry

Josephine Harada

Elliott Meer

Yuan Li

Christopher Joachim O'Keeffe

Pranav Patel

Anthony Makarewicz

Bill Kengli Lin

Eswar Prasad Ramachandran Iyer

Adam Lowe

Shalini Gohil

Joshua Delaney

Vijay Kumar Sreenivasa Gopalan

Solongo B Ziraldo

Phillip Belgrader

Andrew Kohlway

Joseph Francis Shuga

Luigi Jhon Alvarado Martinez

Michael Ybarra Lucero

Kamila Belhocine

Indira Wu

Niranjan Srinivas

Stephane Claude Boutet

Sarah Taylor

Kevin D Ness

Benjamin J Hindson

Donald Masquelier

Mirna Jarosz

Augusto Manuel Tentori

Zeljko Dzakula

Joakim Lundeberg

Steven W Short

Josephine Lee

Felice Alessio Bava

David Sukovich

Francesca Meschi

Jennifer Chew

Cedric Uytingco

David Maurice Cox

Luz Montesclaros

Jerald Sapida

Linda Kvastad

Landon Merrill

Meghan L F Frey

Fernandino Valdecanas

Methods and systems are provided for sample preparation techniques and sequencing of macromolecular constituents of cells and other biological materials.

Methods and systems for analysis

Methods and systems for droplet-based single cell barcoding

Methods and systems for sample preparation techniques that prevent inhibition of reactions such as due to the presence of longer oligonucleotides are presented herein. The methods and systems provided herein allow amplification (e.g., whole genome amplification) and sequencing of chromatin accessible regions of single cells.

Compositions and methods for nucleic acid processing using blocking agents

A sample holder includes a first member featuring a first retaining mechanism configured to retain a first substrate that includes a sample, a second member featuring a second retaining mechanism configured to retain a second substrate that includes a reagent medium, and an alignment mechanism connected to at least one of the first and second members, and configured to align the first and second members such that the sample contacts at least a portion of the reagent medium when the first and second members are aligned.

Imaging system hardware

The present disclosure provides systems and methods for processing or analyzing a sample. Methods may include generating supports (e.g., beads) comprising barcode molecules coupled thereto. A support comprising barcode molecules may be useful for analyzing or processing one or more analytes such as nucleic acid molecules, proteins, and/or perturbation agents.

Systems and methods for sample analysis

Methods and systems for cell and bead processing or analysis are provided. A cell or bead can be subjected to conditions sufficient to change a first characteristic or set of characteristics (e.g., cell or bead size). The cell or bead can further be subjected to conditions sufficient to change a second characteristic or set of characteristics. In some cases, crosslinks are formed within the cell or bead.

Methods and systems for cell and bead processing

The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and analyte characterization. Such polynucleotide processing may be useful for a variety of applications, including analyte characterization by polynucleotide sequencing. The compositions, methods, systems, and devices disclosed herein generally describe barcoded oligonucleotides, which can be bound to a bead, such as a gel bead, useful for characterizing one or more analytes including, for example, protein (e.g., cell surface or intracellular proteins), genomic DNA, and RNA (e.g., mRNA or CRISPR guide RNAs). Also described herein, are barcoded labelling agents and oligonucleotide molecules useful for 'tagging' analytes for characterization.

Methods and systems for processing polynucleotides

The present disclosure provides methods of processing or analyzing a sample. A method for processing a sample may comprise hybridizing a probe molecule to a target region of a nucleic acid molecule (e.g., a ribonucleic acid (RNA) molecule), barcoding the probe-nucleic acid molecule complex, and performing extension, denaturation, and amplification processes. A method for processing a sample may comprise hybridizing first and second probes to adjacent or non-adjacent target regions of a nucleic acid molecule (e.g., an RNA molecule), linking the first and second probes to provide a probe-linked nucleic acid molecule, and barcoding the probe-linked nucleic acid molecule. One or more processes of the methods described herein may be performed within a partition, such as a droplet or well. One or more processes of the methods described herein may be performed on a cell, such as a permeabilized cell.

Methods and systems for characterizing analytes from individual cells or cell populations

The present disclosure provides methods and systems for generation of compositions comprising two or more sets of molecules. Compositions herein may comprise sets of molecules of different types. Sets of molecules may be generated by attachment to supports. Different types of molecules may be used to generate a large number of unique molecules. One or more types of molecules may be used to identify one or more additional types of molecules. Compositions of the present disclosure may be used in, for example, nucleic acid sequencing.

Methods and systems for molecular composition generation

Provided herein are methods and systems for characterizing a nucleic acid molecule from a single cell. A method for characterizing a nucleic acid molecule from a single cell may comprise providing a partition (e.g., droplets or wells) comprising a single cell and a single bead. The single bead may comprise a nucleic acid barcode molecule. A nucleic acid molecule from the single cell and the nucleic acid barcode molecule may be used to generate a barcoded nucleic acid molecule for sequencing, which may be used to determine an epigenetic state or characteristic of the nucleic acid molecule as being associated with the single cell.

Methods and systems for characterizing nucleic acid molecules

The present disclosure provides systems and methods for making a hydrogel comprising a cell, cell nucleus, or one or more components derived from a cell or cell nucleus. A method for making a hydrogel may comprise providing a cell or cell nucleus, a first polymer, wherein the first polymer comprises a plurality of first crosslink precursors, each of the plurality of first crosslink precursors comprising an azide group; providing a second polymer, wherein the second polymer comprises a plurality of second crosslink precursors, each of the plurality of second crosslink precursors comprising an alkyne group; and crosslinking the first polymer and the second polymer via a reaction between a first section of the first crosslink precursors and a second section of the second crosslink precursors, thereby providing the hydrogel comprising the cell or cell nucleus.

Compositions, methods, and systems for bead formation using improved polymers

Compositions, methods, and systems are provided for sample preparation techniques and sequencing of macromolecular constituents derived from a cell (i.e., a cell bead) in a multiplexed reaction. Using the compositions, systems, and methods disclosed herein, the association of the macromolecular constituents with the biological particle from which they are derived and the association of the cell bead with the cell bead sample from which they are derived is maintained.

Methods and systems for multiplexing of droplet based assays

The present disclosure provides methods and systems for cell and bead processing or analysis. A method for processing a cell or bead may include subjecting a bead to conditions sufficient to change a first characteristic or set of characteristics (e.g., cell or bead size). Such a method may further include subjecting the cell or bead to conditions sufficient to change a second characteristic or set of characteristics. In some cases, crosslinks may be formed within the cell or bead.

Growing community of inventors

Hayward, CA, United States of America

Andrew D Price