10x Genomics, Inc.

Bio-rad Laboratories, Inc.

Andrew Kohlway

Katherine Pfeiffer

Andrew D Price

Tarjei Sigurd Mikkelsen

Eswar Prasad Ramachandran Iyer

Luigi Jhon Alvarado Martinez

Ronald Lebofsky

Andrew Hill

Jennifer Chew

Man Cheng

Lucas Frenz

Sean Cater

Paul Eugene Lund

Zachary Burkett

Rob Ray

Methods are provided of assessing whether multiple differently-barcoded primers occur within the same partition.

Methods and compositions for deconvoluting partition barcodes

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 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

Comparison of common sequencing reads from sequencing based on partition-based barcoding can be used to improve sequencing results. Increased loading of barcodes per partition can also improve sequencing results.

Nucleotide sequence generation by barcode bead-colocalization in partitions

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Pleasanton, CA, United States of America

Andrew Kohlway