10x Genomics, Inc.

Eswar Prasad Ramachandran Iyer

Benjamin J Hindson

Yifeng Yin

Andrew D Price

Luigi Jhon Alvarado Martinez

Katherine Pfeiffer

Tarjei Sigurd Mikkelsen

Zachary Bent

Andrew Kohlway

Felice Alessio Bava

Michael Schnall-Levin

Rajiv Bharadwaj

Michael Ybarra Lucero

Augusto Manuel Tentori

Joakim Lundeberg

Steven W Short

Jennifer Chew

Cedric Uytingco

Shalini Gohil

Preyas Shah

David Maurice Cox

Linda Kvastad

Monica Nagendran

Meghan L F Frey

Erik Leonard Henrik Borgstrom

Stefania Giacomello

Alexander Gagnon

Sultan Doganay Tuncer

Eileen Dalin

Jonathan Cheng

Fernandino Valdecanas

Eva Gracia Villacampa

Systems and methods are provided for targeting one or more features in a region of interest, and efficiently removing the features from an array of features. The systems and methods can remove one or more beads that contain analytes, intermediate agents, or a combination thereof, from the region of interest of a substrate by emitting light toward the beads on the substrate.

Spatial targeting of analytes

Provided herein are methods for determining the mislocalization of an analyte by capturing the analyte on an array and measuring the mislocalization distance.

Methods of measuring mislocalization of an analyte

A sample holder includes a first member featuring a first retaining mechanism configured to retain a first substrate that includes a sample, a second member featuring a second retaining mechanism configured to retain a second substrate that includes a reagent medium, and an alignment mechanism connected to at least one of the first and second members, and configured to align the first and second members such that the sample contacts at least a portion of the reagent medium when the first and second members are aligned.

Imaging system hardware

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

The present disclosure relates in some aspects to methods for analyzing a target nucleic acid in a biological sample. In some aspects, the methods involve the use of a set of probe polynucleotides, for example a set of three or more probe polynucleotides, for assessing target nucleic acids. In some aspects, the presence, amount, and/or identity of region of interest in a target nucleic acid is analyzed in situ. Also provided are polynucleotides, sets of polynucleotides, compositions, and kits for use in accordance with the methods.

Sequence analysis using meta-stable nucleic acid molecules

The present disclosure relates to compositions and methods for generating capture probes on a substrate for identifying the location of analytes in a biological sample.

Generating capture probes for spatial analysis

This disclosure relates to compositions and methods for three-dimensional spatial profiling of analytes in a biological sample. The methods include use of a hydrogel comprising one or more polymers that include a phenol moiety, an azide moiety, or an alkyne moiety.

Three-dimensional spatial analysis

Provided herein are methods of determining a location of a target nucleic acid in a biological sample.

Methods of making gene expression libraries

Provided herein are methods of improving sensitivity of spatial detection of an analyte in a biological sample using splint oligonucleotides, circularized second strands, and rolling circle amplification. For example, provided herein are methods of improving sensitivity of spatial detection of an analyte in a biological sample where a splint oligonucleotide hybridizes to a second strand; the second strand is ligated together thereby creating a circularized second strand, rolling circle amplification of the circularized second strand results in generation of an amplified second strand, and all or part of the sequence of the amplified second strand is determined and used to spatially detect the analyte in the biological sample.

Methods for spatial analysis using rolling circle amplification and detection probes

This disclosure relates to methods for spatial profiling of analytes present in a biological sample. Also provided are methods for using spatially barcoded arrays to detect a biological analyte in a cell comprising a small molecule.

Spatial assays with perturbed cells

Provided herein are methods of determining a location of a target analyte in a non-permeabilized biological sample that include the use of a blocking probe.

Methods for determining a location of an analyte in a biological sample

Growing community of inventors

Pleasanton, CA, United States of America

Eswar Prasad Ramachandran Iyer