The present invention relates to methods and devices for amplifying nucleic acid, and, in particular, amplifying so as to generate products on a surface without the use of emulsions. In a preferred embodiment, a plurality of groups of amplified product are generated on the surface, each group positioned in different (typically predetermined) locations on said surface so as to create an array.

Digital microfluidic (DMF) apparatuses, systems, devices and associated fluid manipulation and extraction devices, and methods of using them are presented. The devices may be useful for analysis of clinical, laboratory, chemical, or biological samples. A fluid application and extraction interface device may include a waste reservoir with a fluid trap and a transfer conduit extending through the waste reservoir so that fluid may pass from the transfer conduit into the waste reservoir and be trapped within the waste chamber. A transfer conduit may be configured to double back on itself and to hold a fluid sample. A DMF apparatus may be configured to hold and process large sample volumes.

Various methods and devices for spatial molecular analysis from tissue is provided. For example, a method of spatially mapping a tissue sample is provided with a microarray having a plurality of wells, wherein adjacent wells are separated by a shearing surface; overlaying said microarray with a tissue sample; applying a deformable substrate to an upper surface of said tissue sample; applying a force to the deformable substrate, thereby forcing underlying tissue sample into the plurality of wells; shearing the tissue sample along the shearing surface into a plurality of tissue sample islands, with each unique tissue sample island positioned in a unique well; and imaging or quantifying said plurality of tissue sample islands, thereby generating a spatial map of said tissue sample. The imaging and/or quantifying may use a nucleic acid amplification technique.

Methods and systems for improved labeling and/or de-labeling a molecule or cell in the context of scientific experimentation, industrial applications, and clinical investigation, including the means to repeat the process of labeling and de-labeling in an efficient manner.

An example of a method includes providing a substrate with an exposed surface comprising a first chemical group, wherein the providing optionally comprises modifying the exposed surface of the substrate to incorporate the first chemical group; reacting the first chemical group with a first reactive group of a functionalized polymer molecule to form a functionalized polymer coating layer covalently bound to the exposed surface of the substrate; grafting a primer to the functionalized polymer coating layer by reacting the primer with a second reactive group of the functionalized polymer coating layer; and forming a water-soluble protective coating on the primer and the functionalized polymer coating layer. Examples of flow cells incorporating examples of the water-soluble protective coating are also disclosed herein.

A microfluidic ejection chip includes a silicon substrate having a fluid passageway. The fluid passageway is defined by a silicon sidewall of the silicon substrate that is covered by a permanent passivation layer to protect the silicon sidewall from exposure to an acidic fluid. The permanent passivation layer is retained on the silicon sidewall at a conclusion of etching of the silicon substrate to form the fluid passageway.

In accordance with one embodiment, a method for automatically coordinating droplets for optically controlled microfluidic systems, comprising using light to move one or a plurality of droplets simultaneously, applying an algorithm to coordinate droplet motions and avoid droplet collisions, and moving droplets to a layout of droplets. In another embodiment, a system for automatically coordinating droplets for optically controlled microfluidic systems, comprising using a light source to move one or a plurality of droplets simultaneously, using an algorithm to coordinate droplet motions and avoid droplet collisions, and using a microfluidic device to move droplets to a layout of droplets.

This document provides methods and devices for metering fluids. In some cases, the methods and devices include intersecting channels that include capillary-stop geometries at each intersection point that guides the fluids on a desired path, which is controlled by the opening and closing of valves. For example, a metering channel can intersect a loading channel and intersect an outflow channel and a metering portion can be defined by the geometry of the metering channel between the intersection points.

Using 3D printing, a microwell is formed by providing a plurality of masks, each mask representing a cross-section of a layer of the concave structure. Progressive movement of a projection plane exposes a pre-polymer solution to polymerizing radiation modulated by the masks to define the layers of the microwell, where each layer is exposed for a non-equal exposure period as determined by a non-linear factor. In a preferred embodiment, a first portion of the masks are base layer masks, which are exposed for a longer period than subsequent exposure periods. Shapes of the microwells, which may include circular, square, annular, or other geometric shapes, and their depths, are selected to promote aggregation behavior in the target cells, which may include tumor cells and stem cells.

An example of a flow cell includes a substrate, a plurality of chambers defined on or in the substrate, and a plurality of depressions defined in the substrate and within a perimeter of each of the plurality of chambers. The depressions are separated by interstitial regions. Primers are attached within each of the plurality of depressions, and a capture site is located within each of the plurality of chambers.