A method for making on-flow cell three-dimensional polymer structures includes loading a polymer precursor solution onto a flow cell. The polymer precursor solution includes a monomer, a crosslinker, and a photoinitiator. The flow cell includes at least one channel for receiving the polymer precursor solution. The at least one channel has an upper interior surface and a lower interior surface. The method further includes illuminating the polymer precursor solution through a patterned photomask using a light at a wavelength sufficient to activate the photoinitiator. Activation of the photoinitiator polymerizes at least some of the polymer precursor solution underneath apertures in the patterned photomask and forms three-dimensional polymer structures that extend from the upper interior surface to the lower interior surface of the at least one channel.

A method for patterning flow cell substrates using photo-initiated chemical reactions that includes fabricating a planar waveguide flow cell by forming a layer of light coupling gratings on a glass substrate layer; depositing a core layer on the layer of light coupling gratings; depositing a cladding layer on the core layer; and forming nanowells in the cladding layer; silanizing the cladding layer; coating the silanized cladding layer and nanowells with a first group of reactants; introducing a second group of reactants into the nanowells, wherein the second group of reactants includes a target reactant and a light-sensitive photoinitiator system; coupling a light source to the light coupling gratings and directing light internally within the planar waveguide flow cell for photo-initiating a chemical reaction between the first and second groups of reactants, wherein the photo-initiated chemical reaction covalently binds the target reactant to only the bottom portion of each nanowell.

Systems, computer program products, and methods for using a flow cell array are provided herein. A computer program product includes a computer readable storage medium having program instructions embodied therewith, the program instructions executable by a device to cause the device to deliver multiple items of chemical matter independently to multiple reaction sites of a flow cell array across multiple distinct instances of time; image multiple parallel chemical reactions at the multiple reaction sites of the flow cell array; and record an emission from each of the multiple chemical reactions site.

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.

According to various embodiments, a method is provided that comprises washing an array of DNA-coated beads on a substrate, with a wash solution to remove stacked beads from the substrate. The wash solution can include inert solid beads in a carrier. The DNA-coated beads can have an average diameter and the solid beads in the wash solution can have an average diameter that is at least twice the diameter of the DNA-coated beads. The washing can form dislodged DNA-coated beads and a monolayer of DNA-coated beads. In some embodiments, first beads for forming an array are contacted with a poly(ethylene glycol) (PEG) solution comprising a PEG having a molecular weight of about 350 Da or less. In some embodiments, slides for forming bead arrays are provided as are systems for imaging the same.

Devices and methods for de novo synthesis of large and highly accurate libraries of oligonucleic acids are provided herein. Devices include structures having a main channel and microchannels, where the microchannels have a high surface area to volume ratio. Devices disclosed herein provide for de novo synthesis of oligonucleic acids having a low error rate.

Systems, computer program products, and methods for using a flow cell array are provided herein. A computer program product includes a computer readable storage medium having program instructions embodied therewith, the program instructions executable by a device to cause the device to determine placement of multiple reaction site openings, wherein each reaction site opening is connected to a first sub-surface channel; connect the first sub-surface channel to two or more additional sub-surface channels by multiple vias; and provide a material for multiple reaction sites, wherein an overlap of the multiple reaction site openings and the material delineate the multiple reaction sites.

Apparatus, computer program products, and methods for using a flow cell array are provided herein. A computer program product includes a computer readable storage medium having program instructions embodied therewith, the program instructions executable by a device to cause the device to determine placement of one or more reaction sites on a first component; provide a material for the reaction sites in one or more surface channels of the first component; connect the first component to a second component to form an array, wherein the surface channels of the first component connect the reaction sites with one or more vias, and wherein the second component comprises the vias connected to multiple sub-surface channels; and align the surface channels of the first component with the vias of the second component to form a connection between the first component and the second component.

Systems, computer program products, and methods for using a flow cell array are provided herein. A system includes at least one processor coupled to a memory and configured for delivering multiple items of chemical matter independently to multiple reaction sites of a flow cell array across multiple distinct instances of time; imaging multiple parallel chemical reactions at the multiple reaction sites of the flow cell array; and recording an emission from each of the multiple chemical reactions site.

Systems, computer program products, and methods for using a flow cell array are provided herein. A system includes at least one processor coupled to a memory and configured for determining placement of multiple reaction site openings, wherein each reaction site opening is connected to a first sub-surface channel; connecting the first sub-surface channel to two or more additional sub-surface channels by multiple vias; and providing a material for multiple reaction sites, wherein an overlap of the multiple reaction site openings and the material delineate the multiple reaction sites.