10x Genomics, Inc.

Michael Schnall-Levin

Serge Saxonov

Benjamin J Hindson

Kevin D Ness

Mirna Jarosz

Christopher Hindson

Paul Hardenbol

Rajiv Bharadwaj

Xinying Zheng

Andrew D Price

Anthony Makarewicz

Tarjei Sigurd Mikkelsen

Yifeng Yin

Donald Masquelier

Patrick Marks

Zahra Kamila Belhocine

Yuan Li

Phillip Belgrader

Pranav Patel

Katherine Pfeiffer

Michael Ybarra Lucero

Geoffrey McDermott

Tobias Daniel Wheeler

Jonas Frisen

Bill Kengli Lin

Patrik Stahl

Marlon Stoeckius

Layla Katiraee

Jason Bell

Paul Ryvkin

John R Stuelpnagel

Augusto Manuel Tentori

Zeljko Dzakula

Zachary Bent

Mohammad Rahimi Lenji

Steven W Short

Christina Galonska

Francesca Meschi

Alexander Y Wong

Neil Ira Weisenfeld

Jennifer Chew

Enric Llorens Bobadilla

Maja Marklund

Kamila Belhocine

David Luther Alan Stafford

Jason Underwood

Iain MacCallum

Eswar Prasad Ramachandran Iyer

Jessica Michele Terry

Preyas Shah

Vijay Kumar Sreenivasa Gopalan

Kristina Giorda

Sofia Kyriazopoulou-Panagiotopoulou

Daniel P Riordan

Linda Kvastad

Patrick J Marks

David Jaffe

William Haynes Heaton

Ali R Alemozafar

Landon Merrill

Patrice Mudivarti

Heather Ordonez

Mima Jarosz

Eva Gracia Villacampa

Joakim Lundeberg

Meghan L F Frey

Iain Maccallum

David Stafford

Christopher Martin Hindson

Philip Belgrader

Kevin Dean Ness

The present invention is directed to methods, compositions and systems for analyzing sequence information while retaining structural and molecular context of that sequence information.

Methods and compositions for nucleic acid analysis

The present disclosure provides systems and methods for measuring one or more analytes at the single cell level. In some instances, sequencing of a composite barcode sequence may identify a type of analyte, identify a cell, and determine that the type of analyte originated from the cell. In some instances, a probability that a type of analyte originated from the cell may be determined. Multiple types of analytes may be identified to have originated from the cell, and/or the respective probabilities determined. An analyte may be a protein, such as a surface-bound protein or an internal protein. An analyte may be a metabolite or other small molecule. An analyte may be any constituent of a cell.

Systems and methods for single cell processing

A system for providing structural variation or phasing information is provided. The system accesses a nucleic acid sequence dataset corresponding to a target nucleic acid in a sample. The dataset comprises a header, synopsis, and data section. The data section comprises a plurality of sequencing reads. Each sequencing read comprises a first portion corresponding to a subset of the target nucleic acid and a second portion that encodes an identifier for the sequencing read from a plurality of identifiers. One or more programs in the memory of the system use a microprocessor of the system to provide a haplotype visualization tool that receives a request for structural variation or phasing information from the dataset. The request is evaluated against the synopsis thereby identifying portions of the data section. Structural variation or phasing information is formatted for display in the haplotype visualization tool using the identified portions of the data section.

Systems and methods for visualizing structural variation and phasing information

The present disclosure relates to materials and methods for spatially analyzing nucleic acids that have been fragmented with a transposase enzyme, alone or in combination with other types of analytes.

Method for transposase-mediated spatial tagging and analyzing genomic DNA in a biological sample

Methods and compositions for performing a rolling circle amplification (RCA) reaction using circularized template comprising identifier sequences are provided. Sequencing is performed on the RCA product using a polymerase to incorporate a plurality of cognate nucleotides into the sequencing primer or an extension product thereof to generate an extension product.

Compositions and methods for amplification and sequencing

Methods and compositions for analyzing a library comprising a plurality of amplicons comprising identifier sequences are provided, for example, a library of amplicons in a cell or tissue sample attached to a solid support. For example, amplicons are sequenced using a polymerase to incorporate a plurality of cognate nucleotides into the sequencing primer or an extension product thereof to generate a plurality of extension products.

Compositions and methods for gene expression library analysis

Methods and systems for sorting particles are provided. Methods and systems for sorting cell beads are provided. In some cases, cell beads may be sorted from particles unoccupied with cell derivatives. In some cases, singularly occupied cell beads may be sorted from unoccupied particles and multiply occupied cell beads.

Methods for sorting particles

The present disclosure relates to methods, compositions and systems for haplotype phasing and copy number variation assays. Included within this disclosure are methods and systems for combining the barcode comprising beads with samples in multiple separate partitions, as well as methods of processing, sequencing and analyzing barcoded samples.

Analysis of nucleic acid sequences

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

The invention described herein solves challenges in providing a proficient, rapid and meaningful analysis of sequencing data. Methods and computer program products of the invention allow for a system to receive, analyze, and display sequencing data in real-time. The invention provides solutions to several difficulties encountered in assembling short sequencing-reads, and by doing so the invention improves the worth and significance of sequencing data.

Sequencing methods

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San Francisco, CA, United States of America

Michael Schnall-Levin