Abstract: A fluid delivery device is configured to create a pressure differential across a compartment in which a liquid resides, causing the liquid to flow through the compartment. After a period of time, the fluid delivery device is configured to eliminate the pressure differential and thereby equilibrate the pressure across the compartment, with the use of a pressure equilibration channel that is separate from the compartment. The compartment may contain a packed bed of solid phase particles such as beads. In such case, the pressure differential causes the liquid to flow through the packed bed. The liquid may include chemical reagents or precursors that participate in chemical reactions on or at the solid phase particles. The reactions may relate to chemical synthesis, for example the synthesis of bio-chemicals such as nucleotides.

Abstract: One or more liquids are transferred from a source array to one or more remotely positioned destination sites such as chambers by utilizing one or more movable transfer elements, such as contact pins or capillaries. The source array may include a predetermined organization of addresses at which materials are positioned. One or more materials may be selected for transfer. Based on the selection, one or more addresses may be accessed by the transfer element(s). The addresses may correspond to spots on a surface of the source array. Each spot may be a feature containing one or more (bio)chemical compounds. At the chamber(s), the material(s) may be processed, such by reaction with one or more reagents. The reaction(s) may entail synthesis of one or more desired products. Alternatively, reaction(s) may be performed at the source array, and the product(s) then transferred to the chamber(s).

Abstract: The present invention provides methods for generating a library of synthetic polynucleotides. The present invention also provides methods for generating proteins encoded by the library of synthetic polynucleotides. In addition, provided herein are methods for determining the soluble expression of said proteins. This invention is based, in part, on the discovery of a method for selecting optimal oligonucleotides in combination with performing a phosphorylation reaction, ligation reaction and PCR amplification in a single reaction vessel to produce synthetic polynucleotides in a multiplex manner.

Abstract: One or more liquids are transferred from a source array to one or more remotely positioned destination sites such as chambers by utilizing one or more movable transfer elements, such as contact pins or capillaries. The source array may include a predetermined organization of addresses at which materials are positioned. One or more materials may be selected for transfer. Based on the selection, one or more addresses may be accessed by the transfer element(s). The addresses may correspond to spots on a surface of the source array. Each spot may be a feature containing one or more (bio)chemical compounds. At the chamber(s), the material(s) may be processed, such by reaction with one or more reagents. The reaction(s) may entail synthesis of one or more desired products. Alternatively, reaction(s) may be performed at the source array, and the product(s) then transferred to the chamber(s).

Abstract: The present invention provides methods for generating a library of synthetic polynucleotides. The present invention also provides methods for generating proteins encoded by the library of synthetic polynucleotides. In addition, provided herein are methods for determining the soluble expression of said proteins. This invention is based, in part, on the discovery of a method for selecting optimal oligonucleotides in combination with performing a phosphorylation reaction, ligation reaction and PCR amplification in a single reaction vessel to produce synthetic polynucleotides in a multiplex manner.

Abstract: This disclosure provides, among other things, a nanofluidic device sensing device is provided. In certain embodiments, the device contains: a) a channel comprising a floor and a ceiling, b) an array of charge sensors in the floor and/or ceiling of the channel, arranged along the longitudinal axis of the channel; c) a capture area in the floor and/or ceiling of the channel at the entrance end of the channel; and d) a first electrode and a second electrode, wherein the first and second electrodes are positioned to provide an electrophoretic force along the longitudinal axis of the channel. Other embodiments, e.g., methods, are also described.

Abstract: Provided herein, among other things, is a method comprising: (a) obtaining a mixture of multiple sets of oligonucleotides, wherein the oligonucleotides within each set each comprise a terminal indexer sequence can be assembled to produce a synthon; and (b) hybridizing the oligonucleotide mixture to an array, thereby spatially-separating the different sets of oligonucleotides from one another. Other embodiments are also provided.

Abstract: A method for measuring a property of a binding interaction between a capture agent and a binding partner for the capture agent is provided. In certain embodiments, this method comprises: a) contacting a population of particles that are linked to a capture agent with a substrate comprising a binding partner to produce capture agent/binding partner complexes, wherein the population of particles comprises first particles that are bound to a single molecule of the capture agent and second particles that are bound to two molecules of the capture agent; b) applying a force to the bound support, wherein the force is in a direction that separates the particles from the support; and c) separately measuring the forces required to disassociate the first particles and the second particles from their respective complexes.

Abstract: This disclosure provides, among other things, a nanofluidic device sensing device is provided. In certain embodiments, the device contains: a) a channel comprising a floor and a ceiling, b) an array of charge sensors in the floor and/or ceiling of the channel, arranged along the longitudinal axis of the channel; c) a capture area in the floor and/or ceiling of the channel at the entrance end of the channel; and d) a first electrode and a second electrode, wherein the first and second electrodes are positioned to provide an electrophoretic force along the longitudinal axis of the channel. Other embodiments, e.g., methods, are also described.

Abstract: Provided herein is a set of reagents comprising: a plurality of at least three probe libraries, wherein each library of the plurality comprises one or more probe sets that are each specific for a target; and at least one of the libraries comprises a probe set that is present in another of the libraries. The plurality of libraries can be hybridized to spatially separated targets, simultaneously or sequentially. The identity of a spatially separated target can be determined by identifying which combination of the multiple libraries hybridize thereto.

Abstract: Methods, systems and computer readable media for controlling an instrument in communication with a host computer are provided. Operations of an instrument that must be completed on schedule are controlled via an embedded controller embedded in the instrument. A complete status packet is sent to a host computer from the embedded controller. Periodically, the embedded controller repeats the sending of a complete status packet to the host computer, wherein status values in the complete status packet are updated with each iteration of sending a complete status packet.

Abstract: Methods and systems for identifying and selecting nucleic acid probes for detecting a target with a nucleic acid probe array or comparative genome hybridization microarray, comprising selecting a plurality of potential target sequences, generating a plurality of candidate probes from the target sequences, filtering the plurality of candidate probes by analyzing candidate probes for selected probe properties in silico. Microarrays comprising probes selected by the methods of the invention are particularly useful for comparative genome hybridization and location analysis.

Abstract: Methods, systems and computer readable media for controlling an instrument in communication with a host computer are provided. Operations of an instrument that must be completed on schedule are controlled via an embedded controller embedded in the instrument. A complete status packet is sent to a host computer from the embedded controller Periodically, the embedded controller repeats the sending of a complete status packet to the host computer, wherein status values in the complete status packet are updated with each iteration of sending a complete status packet.

Abstract: Methods and systems for identifying and selecting nucleic acid probes for detecting a target with a nucleic acid probe array or comparative genome hybridization microarray, comprising selecting a plurality of potential target sequences, generating a plurality of candidate probes from the target sequences, filtering the plurality of candidate probes by analyzing candidate probes for selected probe properties in silico. Microarrays comprising probes selected by the methods of the invention are particularly useful for comparative genome hybridization and location analysis.

Abstract: Embodiments of the present invention include methods and systems for analysis of comparative genomic hybridization (“CGH”) data, including CGH data obtained from microarray experiments.

Abstract: Embodiments of the present invention include methods and systems for analysis of comparative genomic hybridization (“CGH”) data, including CGH data obtained from microarray experiments.

Abstract: Methods and compositions for detecting copy number variations between nucleic acid samples are provided. Also provided are kits for practicing methods in accordance with the invention.

Abstract: Systems and methods of obtaining measurement and baseline signals for evaluating assay test strips are described. In one aspect, an assay test strip that has a detection zone with at least one measurement region is held in a respective measurement position for each measurement region in the detection zone. In each measurement position, measurement signals are produced in a measurement data channel in response to light from a respective measurement region of the test strip and baseline signals are produced in a baseline data channel separate from the measurement data channel in response to light from a respective region of the test strip outside of any measurement region. Respective ones of the measurement signals are quantified with respect to corresponding ones of the baseline signals for each measurement position.

Abstract: The nanoscale FET probe comprises a cantilever element and, at one end of the cantilever element, a nanowire that extends from the cantilever element. The nanowire is electrically connected to the cantilever element at at least one of the ends of the nanowire. The nanowire is capable of being coated with molecules of a capture agent along at least part of its length.

Abstract: Methods of reading chemical arrays are provided. Aspects of the methods include reading an array at a first and second detector gain setting to produce linked data sets of an array, where each reading may be made using a different detector gain setting. Aspects of the methods further include extracting features from the linked data sets, where in certain embodiments a merged data set feature extraction protocol is employed. Aspects of the invention further include programming for operating devices, e.g., chemical array readers, as well as readers comprising such programming.