Leland Stanford Junior University

Roche Sequencing Solutions, Inc.

Nodality, Inc.

Other

Rigel Pharmaceuticals, Incorporated

Roche Diagnostics Gmbh

F. Hoffmann-la Roche Ag

Garry P Nolan

Nikolay Samusik

Yury Goltsev

Omar D Perez

Sean Bendall

Jonathan M Irish

Robert M Angelo

Wendy Fantl

Alessandra Cesano

S Michael Rothenberg

Santosh K Putta

David B Rosen

Aileen Cohen

Erik Evensen

David Robert McIlwain

Quan Van Nguyen

Yunqing Ma

Chunfai Lai

Felice Alessio Bava

Karen Sachs

Michael N Rozinov

Erin F Simonds

Julia Kennedy-Darling

Donald G Payan

Crystal L Mackall

Leonard A Herzenberg

Carolina Dallett

Sylvia K Plevritis

Evan Weber

Mohammed N AlQuraishi

Peter Oliver Krutzik

Maeve E O'Huallachain

James L Zehnder

Rachael Hawtin

Drew Hotson

Jason Robert Gotlib

Peng Qiu

Stephen Tracy Oh

Felice-Alessio Bava

Andrew J Gentles

Philip McGarrigle

Jonathan Berek

Yasumichi Hitoshi

Veronica Gonzalez

Steven Fiering

Todd Kinsella

Zinaida Good

Solomon Itani

Bernd Bodenmiller

Tyler J Burns

Harris G Fienberg

Sean C Bendall

David Robert Mcilwain

Jason Ptacek

Matthew B Hale

The invention is a method of simultaneously detecting the presence and spatial location of a target in a tissue sample by attaching an anchor to the target and assembling unique positional barcodes on the anchor. The method enables analyzing cellular targets in 3D.

Spatially oriented quantum barcoding of cellular targets

SNAIL provides cost-efficient detection of specific nucleic acids in single cells, and may be combined with flow cytometry to simultaneously analyze large numbers of cells for a plurality of nucleic acids, e.g. at least one, to up to 5, up to 10, up to 15, up to 20 or more transcripts can be simultaneously analyzed, at a rate of up to about 50, 100, 250, 500 or more cells/second. The methods require only two primers for amplification, and may further include a detection primer.

Multiplexed single molecule RNA visualization with a two-probe proximity ligation system

A method for analyzing planar sample is provided. In some cases the method comprises: (a) labelling the planar sample with a capture agent that is linked to a nucleic acid, wherein the capture agent specifically binds to complementary sites in the planar sample; (b) reading a fluorescent signal caused by extension of a primer that is hybridized to the nucleic acid, using fluorescence microscopy. Several implementations of the method, and multiplexed versions of the same, are also provided.

On-slide staining by primer extension

The invention provides methods, compositions, kits and devices for the detection of target molecules. In some embodiments, the invention allows for multiplexed target molecule detection.

Composition comprising cell origination barcodes for the analysis of both genomic DNA and CDNA from the same cell

A method of analyzing a population of cells is disclosed. In certain embodiments, the method includes i) obtaining an array of cells on a substrate, wherein the cells are labeled with one or more mass tags and are separated from one another, ii) measuring, using secondary ion mass spectrometry (SIMS), the abundance of the one or more mass tags at a plurality of locations occupied by the cells, thereby generating, for each individual cell measured, a set of data, and iii) outputting the set of data for each of the cells analyzed. Also provided herein are systems that find use in performing the subject method. In some embodiments, the system is an automated system for analyzing a population of cells using SIMS.

Single cell analysis using secondary ion mass spectrometry

Provided herein is a composition comprising a mixture of barcoded nucleic acid molecules made from a plurality of cells or cell organelles, wherein the mixture comprises: (a) a population of first nucleic acid molecules each comprising: a sequence of a nucleic acid from a cell or cell organelle, a complement of the sequence, or a barcode identifying the sequence, and a cell-origination barcode; and (b) a population of second nucleic acid molecules each comprising: an epitope specific barcode and a cell-origination barcode. In this composition, the first and second nucleic acid molecules from the same cell or cell organelle have the same cell-origination barcode and first and second nucleic acid molecules from different cells or cell organelles have different cell-origination barcodes.

Composition comprising cell origination barcodes for the analysis of both protein and nucleic acid from the same cell

Provided herein is a method for barcoding, comprising: (a) obtaining multiple populations of cells or cell organelles in a plurality of first volumes, wherein: i. within each first volume the cells or cell organelles comprise nucleic acid molecules that are associated with a first subcode of a set of first subcodes, and ii. in different first volumes the nucleic acid molecules are associated with different first subcodes of the set of first subcodes, (b) pooling the cells or cell organelles, (c) separating the pooled cells or cell organelles into a plurality of second volumes, and (d) associating the nucleic acid molecules with a set of second subcodes in the second volumes, wherein a plurality of the second volumes each receive a different second subcode. This method produces at least some nucleic acid molecules that comprise a first subcode and a second subcode.

Method for barcoding

A method of barcoding is provided. The method comprises: (a) obtaining a population of cells or cell organelles in a first volume, wherein the cells or cell organelles comprise target molecules that are associated with a first assayable oligonucleotide subunit; (b) separating the cells or cell organelles into a plurality of second volumes, wherein at least some of second volumes receive a single cell or cell organelle from the population of cells or cell organelles; and (c) associating a plurality of second assayable oligonucleotide subunits with the first assayable oligonucleotide subunit in the second volumes, wherein at least some of the second volumes each receive a different second assayable oligonucleotide subunit, to produce at least some nucleic acid molecules that comprise a first assayable oligonucleotide subunit and a second assayable oligonucleotide subunit.

Methods of identifying multiple epitopes in cells

The present disclosure generally relates to compositions and methods useful for an adoptive cell therapy. Some embodiments of the disclosure relates to methods for producing a population of lymphocytes enriched in T stem cell memory cells (Tcells). Further provided are compositions containing a substantially pure population of Tcells that are therapeutically effective in treating various cancers, and kits containing such compositions. Methods for treating a subject having or suspected of having a cancer using the compositions and kits as disclosed herein are also provided.

Compositions and methods of expansion of T cell populations

A method of barcoding is provided. The method comprises performing a ligation assay on target nucleic acid molecules that are in or on cells or cell organelles to produce ligation products and adding cell-origination barcodes onto the ligation products or complements thereof by a split-pool barcoding process.

Method for labeling ligation products with cell-specific barcodes II

A method for adding cell origination barcodes onto beads is provided. The method comprises: splitting a pool of beads into a plurality of reaction volumes, appending pre-made oligonucleotides onto the beads in the reaction volumes, wherein at least some of the reaction volumes each receive an oligonucleotide that contains a sequence that is different from the other oligonucleotides added to the reaction volumes, pooling the beads and repeating the splitting, appending and pooling steps one or more times to produce a pool of beads that comprise the cell origination barcodes. In the one or more repeats the oligonucleotides that are appended are added to previously appended oligonucleotides to form the cell origination barcodes.

Barcoded beads and method for making the same by split-pool synthesis

A kit for split-pool barcoding is provided. The kit comprises: a binding agent that binds to a target molecule that is in or on cells or cell organelles and at least two sets of assayable polymer subunit (APS) oligonucleotides. In the kit each set comprises at least 10 unique APS oligonucleotides, the APS oligonucleotides in a set each comprise a sequence that distinguishes the APS oligonucleotides from one another, and the APS oligonucleotides from different sets are configured to link together in an ordered fashion to form all or part of a cell or organelle origination barcode.

Kit for split-pool barcoding target molecules that are in or on cells or cell organelles

A method of barcoding is provided. The method comprises: providing a population of fixed cells or cell organelles in a first reaction volume, hybridizing oligonucleotide probes to target molecules that are in or on the cells or cell organelles in the first reaction volume, splitting the population of cells or cell organelles into a plurality of second reactions volumes, wherein at least some of the second reaction volumes receive a single fixed cell or cell organelle from the population of fixed cells or fixed cell organelles, and adding cell-specific nucleic acid barcodes onto: the oligonucleotide probes, ligation products comprising the oligonucleotide probes, or complements of the oligonucleotide probes or ligation products, in the plurality of second reaction volumes.

Method for labeling ligation products with cell-specific barcodes I

A method for analyzing planar sample is provided. In some cases the method comprises: (a) incubating the planar sample with a capture agent that is linked to an oligonucleotide, wherein the capture agent specifically binds to complementary sites in the planar sample; (b) reading a fluorescent signal caused by extension of a primer that is hybridized to the oligonucleotide, using fluorescence microscopy. Several implementations of the method, and multiplexed versions of the same, are also provided.

Growing community of inventors

San Francisco, CA, United States of America

Garry P Nolan