10x Genomics, Inc.

Felice Alessio Bava

Augusto Manuel Tentori

Rajiv Bharadwaj

Hanyoup Kim

Eswar Prasad Ramachandran Iyer

Andrew D Price

Marlon Stoeckius

Joakim Lundeberg

Zachary Bent

Layla Katiraee

Steven W Short

Yifeng Yin

Christina Galonska

David Sukovich

Caroline Julie Gallant

Jennifer Chew

Cedric Uytingco

David Maurice Cox

James Michael Chell

Jonathan Alles

Linda Kvastad

Amanda Janesick

Meghan L F Frey

Fernandino Valdecanas

Various implementations of electrophoretic systems and instruments are provided to improve electrophoresis and ease of use. Various electrophoretic systems and instruments utilize different electrode designs that can result in uniform electromigration of analytes. The electrophoretic systems and instrumentations optimize the size and/or location of electrodes relative to a sample, thereby increasing uniformity of electric field and reducing or minimizing drift of analyte migration. In addition, the electrophoresis systems and instruments provide a solution to conveniently check for electrical connections in the systems and instruments, and alert users of potential improper electrical connections, prior to performing electrophoresis.

Electrophoresis cassettes and instrumentation

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.

Methods of capturing multiple analytes on a spatial array

Disclosed herein are methods of amplifying an analyte in a biological sample using a bridging oligonucleotide that hybridizes to a captured analyte. The methods disclosed herein include steps of (a) contacting a biological sample with a substrate having capture probes comprising a capture domain and a spatial barcode; (b) hybridizing the analyte to the capture domain; and (c) contacting the analyte to a bridging oligonucleotide comprising (i) a capture-probe-binding sequence, and (ii) an analyte-binding sequence; (d) extending the bridging oligonucleotide; and (e) determining (i) all or a part of the sequence of the analyte, or a complement thereof, and (ii) the spatial barcode, or a complement thereof, and using the determined sequence of (i) and (ii) to determine the location of the analyte in the biological sample.

Increasing efficiency of spatial analysis in a biological sample

The present disclosure provides methods for detecting a nucleic acid molecule involving the use of a signal code sequence which corresponds to said nucleic acid molecule, comprising sequential hybridization of detectably labeled probes to allow detection of a signal code sequence. In particular, the present disclosure provides a method of sequential decoding comprising hybridization-directed quenching of detectable moieties that have already been imaged, allowing the newly added probe to be detected without the need to remove the previously imaged detectable moiety, thus providing an approach that reduces or eliminates the need for damaging probe stripping.

Sequential hybridization and quenching

Provided herein are methods, compositions, and systems for improved in situ detection of analytes and spatial analysis using, e.g., a sequencing readout.

Methods for improved in situ detection of nucleic acids and spatial analysis

Imaging system hardware

Provided herein are methods of preparing a spatial array and methods for associating specific sample analytes with spatial locations in the spatial array. Provided herein are methods for preparing a spatial array using a plurality of primers attached to a substrate to guide a plurality of features to specific locations on the spatial array. In a non-limiting example, a plurality of primers on a substrate can be used to guide a plurality of first features that include capture probes onto the substrate. A plurality of second features that are configured to hybridize to the first features and also include capture probes are added to the substrate.

Methods for preparing high-resolution spatial arrays

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 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 polynucleotides, including one or more polynucleotides (e.g., a detection padlock probe) for detecting a region of interest and one or more polynucleotides (e.g., a control padlock probe) as an internal control, for analyzing target nucleic acids. In some aspects, the presence, amount, and/or identity of a 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.

Methods for internally controlled in situ assays using padlock probes

Provided herein are methods of enhancing spatial resolution of an analyte using sandwich maker system. The methods and systems used herein include a first substrate that includes a plurality of probes that include poly-thymine sequence and a second substrate that includes a plurality of probes comprising a capture domain and a spatial domain.

Methods of enhancing spatial resolution of transcripts

Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample using RNA-templated ligation.

Methods for spatial analysis using RNA-templated ligation

This disclosure relates to methods for increasing capture efficiency of a spatial array using rolling circle amplification of a padlock probe that hybridizes to a capture probe. Also provided are methods for using such spatial arrays to detect a biological analyte in a biological sample.

Increasing capture efficiency of spatial assays

This disclosure relates to compositions and methods for analyzing a tissue section from a biological sample.

Growing community of inventors

Rome, Italy

Felice Alessio Bava