10x Genomics, Inc.

Zachary Bent

Paul Ryvkin

Jessica Michele Terry

Elliott Meer

Tarjei Sigurd Mikkelsen

Andrew D Price

Serge Saxonov

Christopher Hindson

John R Stuelpnagel

Katherine Pfeiffer

Josephine Harada

Niranjan Srinivas

Christopher Joachim O'Keeffe

Phillip Belgrader

Rajiv Bharadwaj

Geoffrey McDermott

Vijay Kumar Sreenivasa Gopalan

Solongo B Ziraldo

Yifeng Yin

Eswar Prasad Ramachandran Iyer

Mohammad Rahimi Lenji

Daniel P Riordan

Michael Ybarra Lucero

Tobias Daniel Wheeler

Jennifer Chew

Indira Wu

Stephane Claude Boutet

Sarah Taylor

Patrick Marks

Augusto Manuel Tentori

Marlon Stoeckius

Joakim Lundeberg

Steven W Short

Felice Alessio Bava

Cedric Uytingco

David Maurice Cox

David Michael Patterson

Linda Kvastad

David Jaffe

Alvaro J Gonzalez Lozano

Meghan L F Frey

Erik Leonard Henrik Borgstrom

Stefania Giacomello

Alexander Gagnon

Meghan Leigh Flanders Frey

Alex Gagnon

Fernandino Valdecanas

Sultan Doganay Tuncer

Eileen Dalin

The present disclosure provides methods and compositions for detecting and spatially locating analyte interactions and gene expression in a biological sample. For example, provided herein are methods of determining a location of at least one analyte in a biological sample using analyte-binding moieties, proximity ligation, and an array including capture probes.

Methods for spatial analysis using proximity ligation

Disclosed are systems and methods for selecting biological particles (e.g., cells or nuclei) based on specific binding to a substrate and single-biological particle measurement of analytes from the substrate-bound biological particles (e.g., cells or nuclei). Single biological particles (e.g., cells or nuclei) from a population of biological particles are captured through their binding to biological particle- (e.g., cell- or nucleus-) and/or molecule-specific biological particle (e.g., cell or nucleus) capture moieties on a substrate. Analytes are released from the single captured biological particles (e.g., cells or nuclei) and bind to analyte-specific barcode molecules associated with the specific biological particle (e.g., cell or nucleus) capture moieties to which a biological particle (e.g., a cell or nucleus) has bound. Analysis of the barcode molecules identifies the bound analytes. The systems and methods are used to select and capture immune cells, such as T-cells that bind specific peptide epitopes through their T-cell receptors (TCRs) or B-cells that bind antigen through their B cell receptors (BCRs). Detection and analysis of barcode molecules that have bound cellular analytes comprising rearranged V(D)J-expressing RNAs from the T-cells or B-cells allows identification of the specific TCR sequences that recognize and bind the specific peptide epitopes or specific BCR sequences that recognize and bind specific antigens.

Systems and methods for detecting analytes from captured single biological particles

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

In some embodiments, provided herein is an integrated assay of a biological sample comprising an in situ assay module and a spatial assay module. The in situ assay comprises analyzing binding between nucleic acid probes and a first analyte at a spatial location of the biological sample. In some embodiments, the method further comprises providing conditions to allow spatially barcoded capture agents to capture a second analyte for analysis in the spatial assay module.

Methods and compositions for integrated in situ spatial assay

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 and systems for producing full-length sequencing information of transcriptomes from single cells or from the bulk. Random ligation and circularization of barcoded or non-barcoded complementary deoxyribonucleic molecules can be used to provide a circular template for amplification and subsequent sequencing.

Transcriptome sequencing through random ligation

The present disclosure provides methods and systems for generating and processing optically tagged beads. A nucleic acid probe comprising a fluorescent tag may be hybridized to a bead to generate an optically tagged bead. The nucleic acid probe hybridized to the optically tagged bead may be detectable by one or more signals and may be substantially unreactive to one or more chemical reactions performed with, or in the presence of, the optically tagged bead.

Systems and methods for processing optically tagged beads

The present disclosure provides methods of generating supports (e.g., beads) comprising barcode molecules coupled thereto. A barcode molecule coupled to a support may comprise a barcode sequence and a functional sequence. A barcode molecule may be generated using two or more ligation reactions in a combinatorial fashion. A support comprising two or more different barcode molecules may be useful for analyzing or processing one or more analytes such as nucleic acid molecules, proteins, and/or perturbation agents.

Functionalized gel beads

Provided herein are methods of detecting target nucleic acids and uses of the same.

Compositions and methods of making gene expression libraries

The present disclosure relates to compositions and methods for generating capture probes on a substrate for identifying the location of analytes in a biological sample.

Generating capture probes for spatial analysis

Provided herein are methods for resetting an array to which a biological sample has been applied that include treating the array with a set of biological sample removal conditions.

Method for resetting an array

Provided herein are methods of determining a location of a target analyte in a non-permeabilized biological sample that include the use of a blocking probe.

Methods for determining a location of an analyte in a biological sample

Provided are systems and methods for analyzing a single cell application or experiment. A set of control beads may be introduced to a biological sample and subjected to the single cell application. The control beads may be configured to mimic analytes in the biological sample, such as a cell or other analyte, and comprise one or more known sequences. The one or more known sequences may be identified to analyze the single cell application.

Systems and methods for quality control in single cell processing

Growing community of inventors

Pleasanton, CA, United States of America

Zachary Bent