Abstract: Systems and methods for conducting designated reactions that include a fluidic network having a sample channel, a reaction chamber, and a reservoir. The sample channel is in flow communication with a sample port. The system also includes a rotary valve that has a flow channel and is configured to rotate between first and second valve positions. The flow channel fluidically couples the reaction chamber and the sample channel when the rotary valve is in the first valve position and fluidically couples the reservoir and the reaction chamber when the rotary valve is in the second valve position. A pump assembly induces a flow of a biological sample toward the reaction chamber when the rotary valve is in the first valve position and induces a flow of a reaction component from the reservoir toward the reaction chamber when the rotary valve is in the second valve position.

Abstract: Provided is an array including a solid support having a surface, the surface having a plurality of wells, the wells containing a gel material, the wells being separated from each other by interstitial regions on the surface, the interstitial regions segregating the gel material in each of the wells from the gel material in other wells of the plurality; and a library of target nucleic acids in the gel material, wherein the gel material in each of the wells comprises a single species of the target nucleic acids of the library. Methods for making and using the array are also provided.

Abstract: Provided is an array including a solid support having a surface, the surface having a plurality of wells, the wells containing a gel material, the wells being separated from each other by interstitial regions on the surface, the interstitial regions segregating the gel material in each of the wells from the gel material in other wells of the plurality; and a library of target nucleic acids in the gel material, wherein the gel material in each of the wells comprises a single species of the target nucleic acids of the library. Methods for making and using the array are also provided.

Abstract: Substrates comprising a functionalizable layer, a polymer layer comprising a plurality of micro-scale or nano-scale patterns, or combinations thereof, and a backing layer and the preparation thereof by using room-temperature UV nano-embossing processes are disclosed. The substrates can be prepared by a roll-to-roll continuous process. The substrates can be used as flow cells, nanofluidic or microfluidic devices for biological molecules analysis.

Abstract: Provided herein is a droplet actuator including (a) first and second substrates separated by a droplet-operations gap, the first and second substrates including respective hydrophobic surfaces that face the droplet-operations gap; (b) a plurality of electrodes coupled to at least one of the first substrate and the second substrate, the electrodes arranged along the droplet-operations gap to control movement of a droplet along the hydrophobic surfaces within the droplet-operations gap; and (c) a hydrophilic or variegated-hydrophilic surface exposed to the droplet-operations gap, the hydrophilic or variegated-hydrophilic surface being positioned to contact the droplet when the droplet is at a select position within the droplet-operations gap.

Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.

Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.

Abstract: A method of registering features in a repeating pattern can include (a) providing an object having a repeating pattern of features and a fiducial; (b) obtaining a target image of the object, wherein the target image includes the repeating pattern of features and the fiducial; (c) comparing the fiducial in the target image to reference data, wherein the reference data includes xy coordinates for a virtual fiducial; and (d) determining locations for the features in the target image based on the comparison of the virtual fiducial in the reference data to the fiducial in the data from the target image. The fiducial can have at least concentric circles that produce three different signal levels. The locations of the features can be determined at a variance of less than 5 ?m.

Abstract: A plurality of isolated microvessels including a plurality of encoded microvessels each having a microbody and a reservoir core. The microbody is configured to separate a biological or chemical substance in the reservoir core from an ambient environment surrounding the microbody. The microbody includes a transparent material that at least partially surrounds the reservoir core and facilitates detection of an optical characteristic of the substance within the reservoir core. The microbody of each microvessel includes an identifiable code that distinguishes individual microvessels of the plurality of encoded microvessels from each other. The plurality of isolated microvessels also includes a plurality of compartments each configured to separate individual microvessels of the plurality of encoded microvessels from each other.

Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.

Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.

Abstract: Provided is an array including a solid support having a surface, the surface having a plurality of wells, the wells containing a gel material, the wells being separated from each other by interstitial regions on the surface, the interstitial regions segregating the gel material in each of the wells from the gel material in other wells of the plurality; and a library of target nucleic acids in the gel material, wherein the gel material in each of the wells comprises a single species of the target nucleic acids of the library. Methods for making and using the array are also provided.

Abstract: A microarray is designed capture one or more molecules of interest at each of a plurality of sites on a substrate. The sites comprise base pads, such as polymer base pads, that promote the attachment of the molecules at the sites. The microarray may be made by one or more patterning techniques to create a layout of base pads in a desired pattern. Further, the microarrays may include features to encourage clonality at the sites.

Abstract: A microarray is designed capture one or more molecules of interest at each of a plurality of sites on a substrate. The sites comprise base pads, such as polymer base pads, that promote the attachment of the molecules at the sites. The microarray may be made by one or more patterning techniques to create a layout of base pads in a desired pattern. Further, the microarrays may include features to encourage clonality at the sites.

Abstract: A plurality of isolated microvessels including a plurality of encoded microvessels each having a microbody and a reservoir core. The microbody is configured to separate a biological or chemical substance in the reservoir core from an ambient environment surrounding the microbody. The microbody includes a transparent material that at least partially surrounds the reservoir core and facilitates detection of an optical characteristic of the substance within the reservoir core. The microbody of each microvessel includes an identifiable code that distinguishes individual microvessels of the plurality of encoded microvessels from each other. The plurality of isolated microvessels also includes a plurality of compartments each configured to separate individual microvessels of the plurality of encoded microvessels from each other.

Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.

Abstract: A method of reading a plurality of encoded microvessels used in an assay for biological or chemical analysis. The method can include providing a plurality of encoded microvessels. The microvessels can include a respective microbody and a reservoir core configured to hold a substance in the reservoir core. The microbody can include a material that surrounds the reservoir core and facilitates detection of a characteristic of the substance within the reservoir core. Optionally, the material can be transparent so as to facilitate detection of an optical characteristic of a substance within the reservoir core. The microbody can include an identifiable code associated with the substance. The method can also include determining the corresponding codes of the microvessels.

Abstract: A method of reading a plurality of encoded microvessels used in an assay for biological or chemical analysis. The method can include providing a plurality of encoded microvessels. The microvessels can include a respective microbody and a reservoir core configured to hold a substance in the reservoir core. The microbody can include a material that surrounds the reservoir core and facilitates detection of a characteristic of the substance within the reservoir core. Optionally, the material can be transparent so as to facilitate detection of an optical characteristic of a substance within the reservoir core. The microbody can include an identifiable code associated with the substance. The method can also include determining the corresponding codes of the microvessels.