The invention relates to a microarray structure that may include a substrate material layer, a continuous three-dimensional (3D) surface layer on the substrate material layer that is capable of functionalisation for use as an array, and an inert material. The structure may include accurately defined and functionalisable isolated areas which are millimeter to nanometer in size. The functionalisable areas may be part of the continuous 3D surface layer and may be isolated by the inert material but interconnected within the structure by the continuous 3D surface layer.

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 herein are formulations, substrates, and arrays. Also disclosed herein are methods for manufacturing and using the formulations, substrates, and arrays. Also disclosed are methods for identifying peptide sequences useful for diagnosis and treatment of disorders, and methods for using the peptide sequences for diagnosis and treatment of disorders, e.g., celiac disorder. In certain embodiments, substrates and arrays comprise a porous layer for synthesis and attachment of polymers or biomolecules.

Embodiments of the present application relate to substrate comprising a surface-bound azido functionalized organosilane wherein the substrate is free or substantially free of a hydrogel or a hydrophilic polymer. Methods of preparing such substrate surface for sequencing applications are also disclosed.

An apparatus includes a flow cell body, a plurality of electrodes, an integrated circuit, and an imaging assembly. The flow cell body defines one or more flow channels and a plurality of wells. Each flow channel is configured to receive a flow of fluid. Each well is fluidically coupled with the corresponding flow channel. Each well is configured to contain at least one polynucleotide. Each electrode is positioned in a corresponding well of the plurality of wells. The electrodes are operable to effect writing of polynucleotides in the corresponding wells. The integrated circuit is operable to drive selective deposition or activation of selected nucleotides to attach to polynucleotides in the wells to thereby generate polynucleotides representing machine-written data in the wells. The imaging assembly is operable to capture images indicative of one or more nucleotides in a polynucleotide.

Registration of a patterned flow cell may utilize fiducials comprising sets or groupings of features (e.g., sites, sample wells, nanowells) having known locations and in which the placement of the features is not in accordance with a periodic pattern or is otherwise distinguishable from the periodic pattern of sites present in non-fiducial regions of the flow cell substrate. In certain embodiments the positioning of the sites that are part of the fiducial represent a break or discontinuity in the periodic pattern of sites that are otherwise present on the surface of a patterned flow cell.

Disclosed herein are methods for forming one or more nanoparticles. The methods include depositing a solution comprising a block copolymer and a metal salt into one or more square pyramidal nanoholes formed in a substrate, and annealing the substrate to provide a single nanoparticle in each of the one or more square pyramidal nanoholes.

An example of a flow cell includes a substrate; a plurality of reactive regions extending along the substrate; and a non-reactive region separating one of the plurality of reactive regions from an adjacent one of the plurality of reactive regions. Each of the plurality of reactive regions includes alternating first and second areas positioned along the reactive region. Each of the first areas includes a first primer set and each of the second areas includes a second primer set that is different than the first primer set. Either adjacent first and second areas directly abut each other, or) the first areas are positioned on protrusions and the second areas are positioned in depressions adjacent to the protrusions.

In an example of a method for making a flow cell, a light sensitive material is deposited over a resin layer including depressions separated by interstitial regions, wherein the depressions overlie a first resin portion having a first thickness and the interstitial regions overlie a second resin portion having a second thickness that is greater than the first thickness. A predetermined ultraviolet light dosage that is based on the first and second thicknesses is directed through the resin layer, whereby the light sensitive material overlying the depressions is exposed to ultraviolet light and the second resin portion absorbs the ultraviolet light, thereby defining an altered light sensitive material at a first predetermined region over the resin layer. The altered light sensitive material is utilized to generate a functionalized layer at the first predetermined region or at a second predetermined region over the resin layer.

In an example of a method for making a flow cell, a metal material is sputtered over a transparent substrate including depressions separated by interstitial regions to form a metal film having a first thickness over the interstitial regions and having a second thickness over the depressions, the second thickness being about 30 nm or less and being at least ⅓ times smaller than the first thickness. A light sensitive material is deposited over the metal film; and the metal film is used to develop the light sensitive material through the transparent substrate to define an altered light sensitive material at a first predetermined region over the transparent substrate. The altered light sensitive material is utilized to generate a functionalized layer at the first predetermined region or at a second predetermined region over the transparent substrate.