An example of a flow cell includes a substrate; a first primer set attached to a first region on the substrate, the first primer set including an un-cleavable first primer and a cleavable second primer; and a second primer set attached to a second region on the substrate, the second primer set including a cleavable first primer and an un-cleavable second primer.

Disclosed is an assay device comprising a high density of wells aligned thereon.

Disclosed herein include methods of specifying sites (e.g., sites for colony formation) on a surface (e.g., a planar surface) and generating a flow cell having the sites specified on a surface. Also disclosed are methods of performing sequencing (e.g., sequencing-by-synthesis and sequencing-by-binding) using the flow cell generated and processing (e.g., aligning, orienting, sorting, and assessing quality) images of the flow cell captured during sequencing.

A miniaturized, automated method for controlled printing of large arrays of nano- to femtoliter droplets by actively transporting mother droplets over hydrophilic-in-hydrophobic (“HIH”) micropatches. The technology uses single or double-plate devices where mother droplets can be actuated and HIH micropatches on one or both plates of the device where the droplets are printed. Due to the selective wettability of the hydrophilic micropatches in a hydrophobic matrix, large nano- to femtoliter droplet arrays are created when mother droplets are transported over the arrays. The parent droplets are moved by various droplet actuation principles. Also, a method using two plates placed one top another while being separated by a spacer. One plate is dedicated to confirming and guiding parent droplets by using hydrophilic patches in a hydrophobic matrix, while the other plate contains HIH arrays for printing of the droplets. When the parent droplet guidance plate is rotated over the plate dedicated to printing of nano- to femtoliter droplets, the droplets are dispensed inside the HIH array utilizing their selective wettability. The methods allow the parent droplets to move over the HIH arrays many times, providing advantages for performing bio-assays or miniaturized materials synthesis in nano- to femtoliter sized droplets. With controlled evaporation of the dispensed droplets of solution, large arrays of printed material can be generated in seconds. The methods provide a nano- to femtoliter droplet printing technique for a wide variety of applications, e.g., protein- or cell-based bio-assays or printing of crystalline structures, suspensions of nanoparticles or microelectronic components.

Provided herein are methods and systems for biochemical analysis, including compositions and methods for processing and analysis of small cell populations and biological samples (e.g., a robotically controlled chip-based nanodroplet platform). In particular aspects, the methods described herein can reduce total processing volumes from conventional volumes to nanoliter volumes within a single reactor vessel (e.g., within a single droplet reactor) while minimizing losses, such as due to sample evaporation.

In one example, a flow cell includes a base support and a protrusion over the base support, where the protrusion is a different material than the base support. The flow cell further includes a first functionalized layer over a first portion of the protrusion, a second functionalized layer over a second portion of the protrusion, and first and second primer sets respectively attached to the first and second functionalized layers.

An example flow cell includes a multi-layer stack including a transparent base support; a patterned sacrificial layer over the transparent base support; and a transparent layer over the patterned sacrificial layer. The flow cell further includes first and second functionalized layers over different portions of the transparent layer, wherein at least one of the first and second functionalized layers aligns with a pattern of the patterned sacrificial layer; and first and second primer sets respectively attached to the first and second functionalized layer.

Disclosed is an assay device comprising a high density of wells aligned thereon.

Provided herein are methods and systems for biochemical analysis, including compositions and methods for processing and analysis of small cell populations and biological samples (e.g., a robotically controlled chip-based nanodroplet platform). In particular aspects, the methods described herein can reduce total processing volumes from conventional volumes to nanoliter volumes within a single reactor vessel (e.g., within a single droplet reactor) while minimizing losses, such as due to sample evaporation.

Disclosed is an assay device comprising a high density of wells aligned thereon.