The present invention provides systems and methods for single-cell RNA sequencing. Embodiments of the methods of the present invention include the steps of: aligning a microwell array on top of a dielectrophoresis (DEP) single-cell-trapping nanowell array; loading a plurality of cells into the nanowell; applying electricity to the nanowell array to trap a quanta of cells equal to a quanta of electrode pairs in at least one nanowell of the nanowell array; discontinuing electricity to the nanowell array in order to transfer the loaded cells from the nanowells to the microwells; loading a plurality of barcoded beads into the microwells so that a single bead occupies each cell-loaded microwell; capturing RNA from the cells and retrieving the RNA-loaded beads; and, sequencing the captured RNA.

A method of manufacturing a device useable in DNA or genome sequencing comprises disposing pairs of electrodes on a substrate, the electrodes within each pair separated by a nanogap; depositing a resist layer over the electrodes; patterning the resist layer to create an exposed region on each electrode at or near each nanogap; roughening the electrode surface within each exposed region using various methods; and exposing the exposed regions to biomolecules, wherein one biomolecule bridges each nanogap of each electrode pair, with each end of each biomolecule bound to the electrodes at each exposed region.

Systems and methods for preparing a nanofluidic LCTEM cell are provided. An exemplary method includes coating a photoresist layer onto a top surface of a silicon nitride substrate; etching channels into the photoresist layer; depositing calcite into the etched channels; removing the photoresist; placing the cell on a holder; connecting a first end of an inlet line to the cell; connecting a second end of the inlet line to an ultrasound transducer configured to generate nanobubbles; and connecting an outlet line to the cell.

The present disclosure provides chips, devices and methods for sequencing a biomolecule. The biomolecule may be DNA, RNA. a protein, or a peptide. The chip comprises a substrate; a first and second fluid chamber; fluid channels connecting the first and second fluid chamber; a first and second electrode disposed on opposing sides of the central fluid channel and having a nanogap therebetween, wherein the width of the nanogap is modulated by confined electrochemical deposition; and a passivation layer disposed on top of the first and second electrodes and the fluid channel.

A method of manipulating microdroplets having an average volume in the range 0.5 femtolitres to 10 nanolitres comprised of at least one biological component and a first aqueous medium having a water activity of a.sub.w1 of less than 1 is provided. It is characterised by the step of maintaining the microdroplets in a water-immiscible carrier fluid which further includes secondary droplets having an average volume less than 25% of the average volume of the microdroplets up to and including a maximum of 4 femtolitres and wherein the volume ratio of carrier fluid to total volume of microdroplets per unit volume of the total is greater than 2:1. The method may be employed for example with microdroplets containing biological cells or with microdroplets containing single nucleoside phosphate such as are prepared in a droplet-based nucleic acid sequencer. The method is suitable for controlling for example cellular, chemical or enzymatic processes and/or microdroplet size in microdroplets or single nucleotide nucleic acid sequencing.

This disclosure provides systems, methods, and apparatus related to optofluidic devices. In one aspect, an optofluidic device includes a substrate, a first nanostructure, a second nanostructure, and a cover. A channel having cross-sectional dimensions of less than about 100 nanometers is defined in a surface of the substrate. The first nanostructure is disposed on the substrate on a first side of the channel and proximate the channel. The second nanostructure is disposed on the substrate on a second side of the channel and proximate the channel. The first and the second nanostructures are disposed on a line that passes across the channel. The cover is disposed on the surface of the substrate.

Sub-millimeter scale three-dimensional (3D) structures are disclosed with customizable chemical properties and/or functionality. The 3D structures are referred to as drop-carrier particles. The drop-carrier particles allow the selective association of one solution (i.e., a dispersed phased) with an interior portion of each of the drop-carrier particles, while a second non-miscible solution (i.e., a continuous phase) associates with an exterior portion of each of the drop-carrier particles due to the specific chemical and/or physical properties of the interior and exterior regions of the drop-carrier particles. The combined drop-carrier particle with the dispersed phase contained therein is referred to as a particle-drop. The selective association results in compartmentalization of the dispersed phase solution into sub-microliter-sized volumes contained in the drop-carrier particles. The compartmentalized volumes can be used for single-molecule assays as well as single-cell, and other single-entity assays.

An assay plate is provided. The assay plate has a body with a plurality of reservoirs formed therein. The reservoirs are shaped and aligned in the body in an orientation to induce drainage of fluids contained therein in a desired direction. A plate array and a funnel array forming an assembly for pooling of samples contained in the assay plate is also provided.

Sample analysis systems and methods using assay surfaces, assay processing units (APUs), assay processing systems (APSs), and laboratory systems are disclosed. An assay surface includes a sample processing component comprising a plurality of regions, including at least one wash region and at least one storage region configured to hold a plurality of solid supports moveable through the regions under a magnetic force, and a detection component configured to receive the solid supports. An APU includes an assay surface receiving component, a magnetic element configured to generate a moveable magnetic field, and one or more processors configured to move the magnetic field. An APS includes one or more assay surfaces and an APU. A laboratory system includes one or more APSs and a controller for parallel processing. Sample processing and detection methods are disclosed with a reduced sample volume and/or shortened processing time and/or higher sensitivity.

Examples relate to techniques for performing a nucleic acid amplification reaction. The method includes generating a nucleic acid solution comprising a plurality of nucleic acid molecules, and combining the nucleic acid solution with a plurality of chamber particles. Each chamber particle includes a chamber for receiving the nucleic acid solution, wherein the chamber receives, at most, one of the plurality of nucleic acid molecules. Each chamber particle also includes reagents for causing a polymerase chain reaction within the chamber. The method further includes inducing nucleic acid amplification to generate an amplified nucleic acid, and performing a detection process to detect the presence of the amplified nucleic acid within the chamber.