10X Genomics, Inc.

Niranjan Srinivas

Paul Ryvkin

Zachary Bent

Jessica Michele Terry

Elliott Meer

Daniel P Riordan

Phillip Belgrader

Serge Saxonov

Rajiv Bharadwaj

Christopher Hindson

John R Stuelpnagel

Katherine Pfeiffer

Andrew D Price

Michael Ybarra Lucero

Tobias Daniel Wheeler

Tarjei Sigurd Mikkelsen

Geoffrey McDermott

Patrick Marks

Mohammad Rahimi Lenji

Josephine Harada

Vijay Kumar Sreenivasa Gopalan

Indira Wu

Solongo B Ziraldo

Stephane Claude Boutet

Christopher Joachim O'Keeffe

Sarah Taylor

Alexander Y Wong

Preyas Shah

Kevin J Wu

Nicolaus Lance Hepler

Nigel Delaney

Alex Gagnon

Chaitanya Aluru

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

Methods for index hopping sequence read filtering are provided. Each read in a plurality of reads from a multiplexed reaction comprises an insert portion, and first (molecular identifier) and second (sample index) non-insert portions. For each of a plurality of hashes, a hash data structure is formed with a representation of each read. Each representation comprises a hash of the first non-insert portion of the corresponding read. Read pairs are identified in the hash data structures. Each pair includes a first and second read sharing a common hash value but differing index values. An entry is added into a heterogeneous data structure, for each such pair, that includes the first and second non-insert portions of the first and second reads of the pair. Reads with first non-insert portion values appearing more than a threshold number of times in the heterogeneous data structure are removed from the plurality of reads.

Systems and methods for index hopping filtering

A visualization system comprising a persistent memory, storing a dataset, and a non-persistent memory implements a pattern visualizing method. The dataset contains discrete attribute values for each first entity of a first type in a plurality of first entities of the first type and discrete attribute values for each first entity of a second type in a plurality of first entities of the second type for each second entity in a plurality of second entities. The dataset is compressed by blocked compression and represents discrete attribute values in both compressed sparse row and column formats. The discrete attribute values are clustered to assign each second entity to a cluster in a plurality of clusters.

Systems and methods for visualizing a pattern in a dataset

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

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Pleasanton, CA, United States of America

Niranjan Srinivas