10x Genomics, Inc.

Katherine Pfeiffer

Tarjei Sigurd Mikkelsen

Andrew D Price

Serge Saxonov

John R Stuelpnagel

Josephine Harada

Christopher Hindson

Tobias Daniel Wheeler

Phillip Belgrader

Rajiv Bharadwaj

Mohammad Rahimi Lenji

Michael Ybarra Lucero

Zachary Bent

Paul Ryvkin

Jessica Michele Terry

Elliott Meer

Andrew Kohlway

Stephane Claude Boutet

Christopher Joachim O'Keeffe

Michael Schnall-Levin

Geoffrey McDermott

Marlon Stoeckius

Yifeng Yin

Caroline Julie Gallant

Solongo B Ziraldo

Sarah Taylor

Pranav Patel

Anthony Makarewicz

Bill Kengli Lin

Zahra Kamila Belhocine

Eswar Prasad Ramachandran Iyer

Vijay Kumar Sreenivasa Gopalan

Luigi Jhon Alvarado Martinez

Francesca Meschi

Niranjan Srinivas

Indira Wu

Andrew Hill

Derek Hunter Vallejo

Carolina Cuellar

Sonya A Clark

Michael Stubbington

Xinying Zheng

Kamila Belhocine

Josephine Lee

David Sukovich

Jason Bell

Luz Montesclaros

Jerald Sapida

Paul Eugene Lund

The present disclosure provides methods and systems for nucleic acid processing. A method for preparing a sequencing set may include providing a template nucleic acid and amplifying the template nucleic acid to provide a complementary nucleic acid. Next, the complementary nucleic acid may be fragmented and barcoded to produce a first set of barcoded fragments comprising a plurality of first barcoded fragments. Next, the plurality of first barcoded fragments may be fragmented to yield a second set of barcoded fragments comprising a plurality of second barcoded fragments.

Systems and methods for nucleic acid preparation

The application provides compositions including engineered reverse transcriptases with at least one altered reverse-transcriptase related activity. The engineered reverse transcriptases or reverse transcription enzymes unexpectedly exhibit one or more altered reverse transcriptase related activities such as but not limited to altered template switching efficiency, altered transcription efficiency or both.

Engineered reverse transcriptase enzymes with enhanced enzymatic activity in nanoliter reaction

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

Systems and methods for identifying and using hybrid/capture probes are provided. cDNA sequences from poly-adenylated mRNA are obtained. Each cDNA sequence in a first subset maps to a gene in a plurality of genes. Each cDNA sequence in a second subset maps to a reference genome portion not represented by the plurality of genes. Each gene has a corresponding plurality of transcripts. The cDNA sequences are exposed to at least 2×10nucleic acid baits between Kand Kresidues long, forming nucleic acid bait—sequence read complexes. Each nucleic acid bait that hybridizes to a cDNA sequence mapping to a gene selectively hybridizes to a first subset or another subset of transcripts corresponding to the gene. Each transcript of each gene is hybridizable to a nucleic acid bait in the at least 2×10nucleic acid baits. The nucleic acid bait—sequence read complexes are captured and analyzed.

Hybrid/capture probe designs for full-length cDNA

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

Provided herein are systems and methods for processing biomolecules (e.g., nucleic acid molecules, proteins) from a sample. A method for processing biomolecules may comprise hybridizing a probe molecule to a target region of a nucleic acid molecule (e.g., a ribonucleic acid (RNA) molecule) and barcoding the probe-nucleic acid molecule complex or derivatives thereof. Such a method can comprise performing a nucleic acid reaction, e.g., extension, denaturation, and amplification. A method for processing a sample may comprise hybridizing probes to (i) target regions of a nucleic acid molecule (e.g., RNA molecule) and (ii) a reporter oligonucleotide of a feature binding group, and barcoding the probe-associated molecules. One or more processes of the methods described herein may be performed within a partition, such as a droplet or well.

Probe-based analysis of nucleic acids and proteins

Reverse transcriptase variants

Provided herein are methods, compositions, and kits for removing a portion of a sequence in a member of a nucleic acid library.

Nucleic acid library methods

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

Growing community of inventors

Berkeley, CA, United States of America

Katherine Pfeiffer