Abstract: Described are microfluidic devices and methods for providing a predetermined number of microspheres or beads, together with a cell, within a fluid droplet being processed. The system may provide each droplet with a single bead and a single cell, and the bead may contain DNA or other reagents for later identifying the specific cell associated with that bead.

Abstract: An example of a biotin-streptavidin cleavage composition includes a formamide reagent and a salt buffer. The formamide reagent is present in the biotin-streptavidin cleavage composition in an amount ranging from about 10% to about 50%, based on a total volume of the biotin-streptavidin cleavage composition. The salt buffer makes up the balance of the biotin-streptavidin cleavage composition. In some examples, the biotin-streptavidin cleavage composition is used to cleave library fragments from a solid support. In other examples, other mechanisms are used to cleave library fragments from a solid support.

Abstract: An example of a kit includes a library preparation fluid, a sample fluid, and an enrichment fluid. The library preparation fluid includes library preparation beads, where each library preparation bead includes a first solid support, and a transposome attached to the first solid support. The fluid includes a genomic deoxyribonucleic acid sequence. The enrichment fluid includes target capture beads, where each target capture bead includes a second solid support, and capture probes attached to the second solid support. Each of the capture probes includes a single stranded deoxyribonucleic acid sequence that is complementary to a targeted region of the genomic deoxyribonucleic acid in the sample fluid.

Abstract: A method includes forming a patterned substrate including a plurality of base pads, using a nano-imprint lithography process. A capture substance is attached to each of the plurality of base pads, optionally through a linker, the capture substance being adapted to promote capture of a target molecule.

Abstract: A method includes grafting oligonucleotides to a flow cell and preparing a library of polynucleotides. Each polynucleotide has been written to contain retrievable information and includes a region complementary to one of the sequencing initiation primers grafted to the flow cell. Each polynucleotide is indexed to permit discrete identification of that polynucleotide and the information it contains over other polynucleotides in the library. Another method includes writing two polynucleotides including two sequences with reverse complementary joining sequences onto a flow cell. One of the polynucleotides is extended to generate a third polynucleotide comprising a sequence that is the combination of the first and second sequences. A fourth polynucleotide is written with a third joining sequence of a fourth sequence.

Abstract: Embodiments provided herewith are directed to self-assembled methods of preparing a patterned surface for sequencing applications including, for example, a patterned flow cell or a patterned surface for digital fluidic devices. The methods utilize photolithography to create a patterned surface with a plurality of microscale or nanoscale contours, separated by hydrophobic interstitial regions, without the need of oxygen plasma treatment during the photolithography process. In addition, the methods avoid the use of any chemical or mechanical polishing steps after the deposition of a gel material to the contours.

Abstract: A method includes forming a patterned substrate including a plurality of base pads, using a nano-imprint lithography process. A capture substance is attached to each of the plurality of base pads, optionally through a linker, the capture substance being adapted to promote capture of a target molecule.

Abstract: Embodiments provided herewith are directed to self-assembled methods of preparing a patterned surface for sequencing applications including, for example, a patterned flow cell or a patterned surface for digital fluidic devices. The methods utilize photolithography to create a patterned surface with a plurality of microscale or nanoscale contours, separated by hydrophobic interstitial regions, without the need of oxygen plasma treatment during the photolithography process. In addition, the methods avoid the use of any chemical or mechanical polishing steps after the deposition of a gel material to the contours.

Abstract: Provided is a surface having metal regions and an interstitial region having a composition that differs from the metal regions, wherein a continuous gel layer coats the surface across the metal regions and the interstitial regions. Nucleic acids or other analytes can be attached to the continuous gel layer such that a greater amount is attached over the metal regions than over the interstitial region. Also provided are methods for making such surfaces. Methods are also provided for making an array of nucleic acids or other analytes using such surfaces.

Abstract: An example of a nucleic acid extraction material includes a substrate. The nucleic acid extraction material also includes a polycation bonded to at least a portion of a surface of the substrate. The polycation consists of a polymer of a quaternized monomer selected from the group consisting of a quaternized 1-vinylimidazole monomer and a quaternized dimethylaminoethyl methacrylate monomer, or a copolymer of a neutral monomer and the quaternized monomer.

Abstract: Provided is a surface having metal regions and an interstitial region having a composition that differs from the metal regions, wherein a continuous gel layer coats the surface across the metal regions and the interstitial regions. Nucleic acids or other analytes can be attached to the continuous gel layer such that a greater amount is attached over the metal regions than over the interstitial region. Also provided are methods for making such surfaces. Methods are also provided for making an array of nucleic acids or other analytes using such surfaces.

Abstract: An example of a flow cell includes a substrate, which includes nano-depressions defined in a surface of the substrate, and interstitial regions separating the nano-depressions. A hydrophobic material layer has a surface that is at least substantially co-planar with the interstitial regions and is positioned to define a hydrophobic barrier around respective sub-sets of the nano-depressions.

Abstract: An example of a sequencing kit includes a flow cell, an encapsulation matrix precursor composition, and a radical initiator. The flow cell includes a plurality of chambers and primers attached within each of the plurality of chambers. The encapsulation matrix precursor composition consists of a fluid, a monomer or polymer including a radical generating and chain elongating functional group, a radical source, and a crosslinker. The radical initiator is part of the encapsulation matrix precursor composition or is a separate component.

Abstract: 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.

Abstract: A detection apparatus that includes (a) an array of responsive pads on a substrate surface; (b) an array of pixels, wherein each pixel in the array has a detection zone on the surface that includes a subset of at least two of the pads; and (c) an activation circuit to apply a force at a first and second pad in the subset, wherein the activation circuit is configured to apply a different force at the first pad compared to the second pad, and wherein the activation circuit has a switch to selectively alter the force at the first pad and the second pad.

Abstract: Implementations of a method for seeding sequence libraries on a surface of a sequencing flow cell that allow for spatial segregation of the libraries on the surface are provided. The spatial segregation can be used to index sequence reads from individual sequencing libraries to increase efficiency of subsequent data analysis. In some examples, hydrogel beads containing encapsulated sequencing libraries are captured on a sequencing flow cell and degraded in the presence of a liquid diffusion barrier to allow for the spatial segregation and seeding of the sequencing libraries on the surface of the flow cell. Additionally, examples of systems, methods and compositions are provided relating to flow cell devices configured for nucleic acid library preparation and single cell sequencing. Some examples include flow cell devices having a hydrogel with genetic material disposed therein, and which is retained within the hydrogel during nucleic acid processing.

Abstract: Disclosed are methods and systems concerning flow cells for sequencing a nucleic acid sample that may be characterized by the following components: a substrate having an inner surface facing a library sequencing region, and an outer surface; a plurality of a plurality of forward and reverse amplification primers immobilized over the inner surface and providing a nucleic acid library capture surface of the library sequencing region; a plurality of electrodes disposed along the inner surface directly under at least some of the forward and reverse amplification primers, and configured to provide, when charged, an electric field through the library capture surface and into the library sequencing region; electrical leads connected to the plurality of electrodes to permit the electrodes to be independently addressable; and fluidic couplings configured to deliver a plurality of nucleic acid libraries to the flow cell during different time periods.

Abstract: Described are microfluidic devices and methods for providing a predetermined number of microspheres or beads, together with a cell, within a fluid droplet being processed. The system may provide each droplet with a single bead and a single cell, and the bead may contain DNA or other reagents for later identifying the specific cell associated with that bead.

Abstract: Disclosed are methods and systems concerning flow cells for sequencing a nucleic acid sample that may be characterized by the following components: (a) a substrate having an inner surface facing a library sequencing region, and an outer surface; (b) a plurality of a plurality of forward and reverse amplification primers immobilized over the inner surface and providing a nucleic acid library capture surface of the library sequencing region; (c) a plurality of electrodes disposed along the inner surface directly under at least some of the forward and reverse amplification primers, and configured to provide, when charged, an electric field through the library capture surface and into the library sequencing region; (d) electrical leads connected to the plurality of electrodes to permit the electrodes to be independently addressable; and (e) fluidic couplings configured to deliver a plurality of nucleic acid libraries to the flow cell during different time periods.

Abstract: Embodiments provided herewith are directed to self-assembled methods of preparing a patterned surface for sequencing applications including, for example, a patterned flow cell or a patterned surface for digital fluidic devices. The methods utilize photolithography to create a patterned surface with a plurality of microscale or nanoscale contours, separated by hydrophobic interstitial regions, without the need of oxygen plasma treatment during the photolithography process. In addition, the methods avoid the use of any chemical or mechanical polishing steps after the deposition of a gel material to the contours.