Takara Bio Usa, Inc.

Agilent Technologies, Inc.

University of California

Maithreyan Srinivasan

Jude Menlo Dunne

Thomas David Schaal

Alain-Albert Mir

Syed A Husain

Bradley L Griswold

Chun-Wah Lin

Patricio Espinoza

Michael Slater

Shanavaz Loharasp D Nasarabadi

Glenn Hein

Russell S Cole

Adam R Abate

Siyuan Chen

Olof John Ericsson

Henrik Johansson

Jeremy Lackey

Patricio A Espinoza Vallejos

Patricio A Espinoza-Vallejos

Fredrik Dahl

Justin Madrigal

Christian Siltanen

Alain Mir

Methods for selectively combining discrete entities including, e.g. cells, reagents, drugs, hydrogels, extracellular matrices beads, particles, biological materials, media, or a combination thereof, are provided. In certain aspects, the methods include sorting a plurality of discrete entities and trapping two or more discrete entities for a time sufficient for the two or more discrete entities to combine to form a combined discrete entity. In certain aspects, the methods include making the plurality of discrete entities. In certain aspects, the methods include detecting or analyzing the discrete entities, e.g. via optical detection. In certain aspects, the methods include manipulating or analyzing the combined discrete entity or a component therein, e.g. imaging, sequencing, culturing, e.g., three-dimensional culturing, and measuring cell-cell interactions. Systems and devices for practicing the subject methods are also provided.

Platform for the deterministic assembly of microfluidic droplets

The present disclosure provides methods, compositions, and systems employing blocked primers. Aspects of the disclosure include providing a blocked primer reaction mixture that includes a blocked primer and a template nucleic acid component from a single cell; unblocking the blocked primer to produce an active primer reaction mixture and subjecting the activated primer reaction mixture to primer extension conditions, such as nucleic acid amplification conditions.

Methods and compositions employing blocked primers

The present disclosure provides methods, device, assemblies, and systems for dispensing and visualizing single cells. For example, provided herein are systems and methods for dispensing a dispense volume into a plurality of wells of a multi-well device, where, on average, a pre-determined number of cells (e.g., 1-20) are present in the dispense volume, and determining, via a cellular label, the number of cells present in each of the plurality of wells. Such dispensing and cell detection may be repeated a number of times with respect to wells identified as having less than the pre-determined number of cells in order increase the number wells in the multi-well device containing the desired number (e.g., a single cell).

Method for rapid accurate dispensing, visualization and analysis of single cells

Provided herein are systems and methods for whole genome amplification and sequencing. In particular, provided herein are systems and methods for detection of nucleic acid variants (e.g., rare variants) in limited samples.

Systems and methods for whole genome amplification

The present invention provides methods, systems, assemblies, and articles for capturing single cells with a polymer capture film. In certain embodiments, the polymer capture films comprise a plurality of individual channels with top and bottom openings, where the channels are dimensioned such that a single cell is: i) is captured inside the channel, partially or substantially occluding the channel, when negative pressure is provided to the bottom opening; or ii) is captured by the top opening, but does not enter the channel, when negative pressure is provided to the bottom opening. In some embodiments, the channels of the polymer capture film align with the wells of a multi-well chip such that the cell, or the contents of the single cell, may be transferred to a corresponding well.

Single cell capture with polymer capture films

The present invention provides methods, systems, assemblies, and articles for capturing single cells with a capture chip. In certain embodiments, the capture chip comprises a substrate comprising a plurality of cell-sized dimples or wells that each allow a single cell to be captured from a cell suspension. In some embodiments, the dimples or wells of the capture chip align with the holes or wells of a multi-well through-hole chip, and/or a multi-well chip, such that the cell, or the contents of the single cell, may be transferred to a corresponding well of the multi-well chip. In particular embodiments, the bottom of each dimple or well of the capture chip has a positive electrical charge sufficient to attract cells from a cell suspension flowing over the dimples or wells.

Single cell capture with capture chips

The invention provides novel oligonucleotide probes that have dendrimeric dyes useful for detecting and analyzing biological samples, and compositions and methods thereof. The dendrimeric dye-containing oligonucleotide probes are useful for high sensitivity fluorescence in situ hybridization (FISH) of nucleic acids such as DNA and RNA.

Dendrimeric dye-containing oligonucleotide probes and methods of preparation and uses thereof

This disclosure provides a method for adding an adaptor to a genomic sequence by invasive cleavage, as well as a kit for performing the method. In some embodiments, the method comprises: a) hybridizing genomic DNA to an adaptor comprising a double stranded region and a single stranded region comprising a 5' overhang to produce a substrate for a flap endonuclease; b) cleaving the substrate using the flap endonuclease; c) ligating the recessed end of the double stranded region to the fragment to produce an adaptor-ligated DNA; d) intramolecularly ligating the ends of the adaptor-ligated DNA to produce a circular DNA molecule; and e) enzymatically processing the circular DNA molecule using an oligonucleotide that hybridizes to the adaptor and an enzyme. A kit for performing the method is also provided.

Addition of an adaptor by invasive cleavage

Growing community of inventors

Palo Alto, CA, United States of America

Maithreyan Srinivasan