Harvard College

Bio-rad Laboratories, Inc.

Brandeis University

Universitat Augsburg

Triplebar Bio, Inc.

Hercules Corporation

Bio-rad Europe Gmbh

Centre National De La Recherche Scientifique

Raindance Technologies, Inc.

Université Louis Pasteur De Strasbourg

Jeremy Agresti

George M Church

Darren Roy Link

Amy Rowat

David A Weitz

Ronald Lebofsky

Morten Sommer

Gautam Dantas

Jin-Woong Kim

Liang-Yin Chu

Seth Fraden

Yanwei Jia

Seila Selimovic

Adam R Abate

Christian Boehm

Michael Weiner

Keunho Ahn

Hakim Boukellal

George Karlin-Neumann

Lucas Frenz

Achim Wixforth

Thomas Franke

Lothar Schmid

Tony Hung

Kevin G Hoff

Claudia Litterst

Samantha Cooper

Christoph Merten

John Brian Hutchison

Sarah Koester

Andres Ornelas Vargas

Svilen Tzonev

Abdeslam El Harrak

Nick Heredia

Andrew Utada

Henry Chong

Michael P Weiner

Valérie Taly

George Karlin-neumann

Rodrigo E Guerra

Oliver Jon Miller

Christian Holtze

Andrew S Griffiths

Michaël Rychellynck

Jean-Christophe Baret

Andrews Griffiths

Methods and compositions are described for single cell resolution, quantitative proteomic analysis using high throughput sequencing.

Digital protein quantification

The present invention generally relates to droplets and/or emulsions, such as multiple emulsions. In some cases, the droplets and/or emulsions may be used in assays, and in certain embodiments, the droplet or emulsion may be hardened to form a gel. In some aspects, a heterogeneous assay can be performed using a gel. For example, a droplet may be hardened to form a gel, where the droplet contains a cell, DNA, or other suitable species. The gel may be exposed to a reactant, and the reactant may interact with the gel and/or with the cell, DNA, etc., in some fashion. For example, the reactant may diffuse through the gel, or the hardened particle may liquefy to form a liquid state, allowing the reactant to interact with the cell. As a specific example, DNA contained within a gel particle may be subject to PCR (polymerase chain reaction) amplification, e.g., by using PCR primers able to bind to the gel as it forms. As the DNA is amplified using PCR, some of the DNA will be bound to the gel via the PCR primer. After the PCR reaction, unbound DNA may be removed from the gel, e.g., via diffusion or washing. Thus, a gel particle having bound DNA may be formed in one embodiment of the invention.

Assays and other reactions involving droplets

The present invention generally relates to droplets and/or emulsions, such as multiple emulsions. In some cases, the droplets and/or emulsions may be used in assays, and in certain embodiments, the droplet or emulsion may be hardened to form a gel. For example, a droplet may be hardened to form a gel, where the droplet contains a cell, DNA, or other suitable species. The gel may be exposed to a reactant, and the reactant may interact with the gel and/or with the cell, DNA, etc., in some fashion. For example, the reactant may diffuse through the gel, or the hardened particle may liquefy to form a liquid state, allowing the reactant to interact with the cell. As the DNA is amplified using PCR, some of the DNA will be bound to the gel via the PCR primer.

Methods and compositions are provided herein for preparing high-throughput cDNA sequencing libraries.

Second strand direct

Improved multiple displacement amplification (MDA) reagents and methods are provided.

MDA using bead oligonucleotide

The present invention is generally related to systems and methods for producing a plurality of droplets. The droplets may contain varying species, e.g., for use as a library. In some cases, the fluidic droplets may be rigidified to form rigidified droplets (e.g., gel droplets). In certain embodiments, the droplets may undergo a phase change (e.g., from rigidified droplets to fluidized droplets), as discussed more herein. In some cases, a species may be added internally to a droplet by exposing the droplet to a fluid comprising a plurality of species.

Creation of libraries of droplets and related species

Provided herein are systems and methods for screening desirable biological variants using a high-throughput integrated system. The integrated system may be configured to input a plurality of parameters from functional studies of biological variants under applied conditions, in conjunction with integrated libraries of biological variants, and filter the inputs to produce desirable biological variants based on an input performance requirement. The system may output optimized strains, molecules, or novel molecules expected to have a desirable functional characteristic. Accordingly, the methods and systems disclosed herein enable multi-parametric studies of biological diversity and conditional diversity in systems biology.

Multiparametric discovery and optimization platform

Provided herein are compositions and methods for generating phase-shift barcode oligonucleotides for library construction for next-generation sequencing. In some cases, barcode oligonucleotides are attached to particles or beads. Also provided are methods and kits for using the phase-shift barcode oligonucleotides in sequencing assays.

Synthesizing barcoding sequences utilizing phase-shift blocks and uses thereof

Methods and compositions are provided for making and using uniquely tagged target nucleic acid molecules.

Molecular barcoding

Methods and compositions for maintaining DNA contiguity for sequencing is provided. For example, a plurality of partitions is provided comprising a bead, a forward primer oligonucleotide cleaved from the bead, the forward primer oligonucleotide having a bead-specific barcode and a 3' end specific for and complementary to a first or second adaptor; a reverse primer oligonucleotide having a 3&#x2032; end complementary to the first or second adaptor, wherein the forward primer 3&#x2032; end and the reverse primer 3&#x2032; end are complementary to different adaptors selected from the first adaptor and the second adaptor; and fragments of genomic DNA reacted with an adapter-loaded tagmentase such that the DNA fragments comprise breakpoints in the fragments and an inserted adaptor at the break points, wherein the tagmentase binds the breakpoints to form linked DNA segments in the form of DNA segment-first adaptor tagmentase second adaptor-(DNA segment-first adaptor tagmentase second adaptor)n-DNA segment, where n is any integer and '-' indicates a covalent linkage.

Droplet tagging contiguity preserved tagmented DNA

Microfluidic structures and methods for manipulating fluids, fluid components, and reactions are provided. In one aspect, such structures and methods can allow production of droplets of a precise volume, which can be stored/maintained at precise regions of the device. In another aspect, microfluidic structures and methods described herein are designed for containing and positioning components in an arrangement such that the components can be manipulated and then tracked even after manipulation. For example, cells may be constrained in an arrangement in microfluidic structures described herein to facilitate tracking during their growth and/or after they multiply.

Manipulation of fluids, fluid components and reactions in microfluidic systems

Growing community of inventors

Richmond, CA, United States of America

Jeremy Agresti