10x Genomics, Inc.

Vijay Kumar Sreenivasa Gopalan

Andrew D Price

Tarjei Sigurd Mikkelsen

Zachary Bent

Paul Ryvkin

Jessica Michele Terry

Phillip Belgrader

Serge Saxonov

Rajiv Bharadwaj

Christopher Hindson

John R Stuelpnagel

Katherine Pfeiffer

Geoffrey McDermott

Mohammad Rahimi Lenji

Josephine Harada

Elliott Meer

Jasper Staab

Christopher Joachim O'Keeffe

Michael Ybarra Lucero

Tobias Daniel Wheeler

Kevin J Wu

Jeffrey Clark Mellen

Indira Wu

Solongo B Ziraldo

Niranjan Srinivas

Stephane Claude Boutet

Sarah Taylor

Nicolaus Lance Hepler

Michael Schnall-Levin

Patrick Marks

Zeljko Dzakula

Zahra Kamila Belhocine

Yifeng Yin

Arundhati Shamoni Maheshwari

David Jaffe

Li Wang

Jessica Hamel

Systems and methods for visualizing patterns in discrete attribute value datasets are provided. A dataset comprises a discrete attribute value for each gene in a plurality of genes, for each cell in a plurality of cells. The dataset further comprises ATAC counts for each ATAC peak in a plurality of peaks, for each of the cells. Cells are assigned cluster groups in a first plurality of cluster groups based on a first clustering of discrete attribute values for the genes across the cells. Cell are also assigned cluster groups in a second plurality of cluster groups based on a second clustering of ATAC fragment count values for the ATAC peaks across the cells. A projection of the cells uses one of the first or second cluster group assignments. There is indicated, for each cell within the projection, membership in the other of the first or second cluster group assignments.

Systems and methods for joint interactive visualization of gene expression and DNA chromatin accessibility

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

A dataset is obtained comprising data blocks, each representing a different characteristic, for a plurality of cells across a plurality of bins, each bin representing a different portion of a reference sequence. Cells are clustered on one such characteristic across the bins thereby forming a tree that includes root, intermediate, and terminal nodes, where the cells are terminal nodes and intermediate nodes have daughter nodes, themselves being intermediate nodes or a cell. A subset of the tree is displayed that includes the root and leaves, each leaf representing an intermediate node or a cell. A heat map of the characteristic is also displayed, the map including a segment for each leaf, across the bins. When a segment represents an intermediate node, it is an average of the characteristic across daughters of the node. Graphs of characteristics for the root across the bins are also displayed.

Systems and methods for visualization of single-cell resolution characteristics

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

Systems and methods for inferring a status of a cell population are provided. Described techniques allow deconvolving a first clonal population comprising a first plurality of cells of a species, wherein nucleic acid sequence reads from each cell in the first plurality of cells are obtained. The nucleic acid sequence reads are mapped into bins representing portions of a reference genome, and a pattern of sequence read counts for each cell across the multiple bins is used to assign a cell to a group, thereby inferring a mitotic status of the cell. The assignment of nucleic acid sequence reads into bins is also be used for segregating cells into classes based on a status of a certain biological marker in each cell. Comparison of sequence read counts for a subset of bins across the cell classes allows evaluating effect of a compound on a cell status.

Systems and methods for inferring cell status

The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing.

Growing community of inventors

Santa Clara, CA, United States of America

Vijay Kumar Sreenivasa Gopalan