10x Genomics, Inc.

Geoffrey McDermott

Xinying Zheng

Francesca Meschi

Andrew D Price

Zahra Kamila Belhocine

Michael Schnall-Levin

Katherine Pfeiffer

Zachary Bent

Paul Ryvkin

Jessica Michele Terry

Solongo B Ziraldo

Phillip Belgrader

Serge Saxonov

Christopher Hindson

John R Stuelpnagel

Tarjei Sigurd Mikkelsen

Mohammad Rahimi Lenji

Josephine Harada

Elliott Meer

Jason Bell

Vijay Kumar Sreenivasa Gopalan

Christopher Joachim O'Keeffe

Rajiv Bharadwaj

Michael Ybarra Lucero

Tobias Daniel Wheeler

Felice Alessio Bava

Indira Wu

Niranjan Srinivas

Stephane Claude Boutet

Sarah Taylor

Shea Thompson Lance

Kamila Belhocine

Wyatt James McDONNELL

Meghan Leigh Flanders Frey

Michael John Terry Stubbington

Disclosed are methods, compositions and kits for contacting a sample containing a biological particle with a catalyst associated with or attached to a support. The biological particle may be cells and/or nuclei. The catalyst may be an enzyme configured to digest an extracellular molecule, such as an extracellular biological molecule, including extracellular nucleic acid molecules. In some examples, the biological particle is an aggregate of cells that is processed to single cells with a nuclease that is attached to a bead support. The bead and nuclease may subsequently be removed from the system. The single cells that result from the method can be used in single cell-based droplet systems for obtaining genome or transcriptome profiles of single cells.

Methods, kits, and compositions for processing extracellular molecules

The present disclosure relates to methods, compositions and systems for droplet processing. For example, a method can include (a) partitioning a plurality of cells into a plurality of aqueous droplets, wherein an aqueous droplet of the plurality of aqueous droplets comprises a cell of the plurality of cells; and delivering a micellized lysis agent to the cell in the aqueous droplet.

Analysis of nucleic acid sequences

The present disclosure relates in some aspects to methods and compositions for assessing the target binding capacity of a binding molecule, such as an antigen binding molecule, e.g., a monoclonal antibody. In some embodiments, provided herein is a method of analyzing binding of a barcode-labeled antibody to a target antigen expressed by a cell, wherein cells expressing the candidate antigens are partitioned and wherein detection of the barcoded nucleic acid molecule is indicative of the binding between the antibody or antigen-binding fragment thereof and the candidate antigen or epitope of the cell.

Methods and compositions for analyzing target binding of molecules

The present disclosure relates to methods, compositions and systems for droplet processing. For example, methods can include (a) providing a first emulsion comprising a first droplet population, wherein droplets of the first droplet population comprise a lysis reagent, and a second emulsion comprising a second droplet population, wherein a droplet of the second droplet population comprises i) a cell or a nucleus, and ii) a plurality of nucleic acid barcode molecules; (b) subjecting the first emulsion and second emulsion to conditions sufficient to transfer the lysis reagent to the second droplet population via micelles comprising the lysis reagent; and (c) lysing the cell or the nucleus within the droplet of the second droplet population with the lysis reagent.

The present disclosure provides methods and systems for nucleic acid preparation and/or analysis. Nucleic acids may be derived from one or more cells. Nucleic acid preparation may comprise generating nucleic acid molecules of varying lengths. Nucleic acid analysis may comprise identifying nucleic acid sequence information with nucleosome position information.

Methods and systems for nucleic acid preparation and chromatin analysis

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

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 compositions, methods, systems, and devices for polynucleotide processing and analyte characterization from a single cell. Such polynucleotide processing may be useful for a variety of applications. 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) and chromatin (e.g., accessible chromatin).

Methods and systems for analysis of chromatin

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

Methods and systems for sample preparation techniques that allow amplification (e.g., whole genome amplification) and sequencing of chromatin accessible regions of single cells are provided. The methods and systems generally operate by forming or providing partitions (e.g., droplets) including a single biological particle and a single bead comprising a barcoded oligonucleotide. The preparation of barcoded next-generation sequencing libraries prepared from a single cell is facilitated by the transposon-mediated transposition and fragmentation of a target nucleic acid sequence. The methods and systems may be configured to allow the implementation of single-operation or multi-operation chemical and/or biochemical processing within the partitions.

Single cell analysis of transposase accessible chromatin

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Livermore, CA, United States of America

Geoffrey McDermott