Abstract: A method, apparatus and computer program product, for fabricating an array of biopolymers on a substrate. The method uses a biopolymer or biomonomer fluid and a drop dispenser having a chamber into which the fluid is loaded and an orifice communicating with the chamber from which the fluid is dispensed. The method includes, when the chamber is loaded, applying a prime pressure to the fluid which varies over a range sufficient to move fluid within the drop dispenser but insufficient to cause fluid to be dispensed from the orifice. Drops are dispensed from the dispenser to the substrate so as to form the array.

Abstract: An apparatus and method for separating and identifying chemical moieties. The apparatus employs a micro array device coupled to a detector such as a mass spectrometer system. The apparatus both separates and identifies target molecules without the requirement of extraneous tags or fluorescent markers. Methods for using the apparatus are also disclosed.

Abstract: Method and system for partitioning pixels of a region within a scanned, digital image of a microarray into a set of feature pixels and a set of background pixels based on a difference between the intensity variance or noise within a subregion of pixels corresponding to a feature and the variance of background pixels. In one embodiment of the present invention, a standard deviation and mean for the pixel intensities within a microarray-image region are computed, assuming a normal distribution for the noise, and are used to compute a one-dimensional computed probability distribution function for the pixels in the microarray-image region. The one-dimensional, computed probability distribution is generally bimodal, with pixels within a first peak at a lower-probability region of the computed probability distribution corresponding to feature pixels and pixels within a second, larger peak at a relatively larger computed probability corresponding to background pixels.

Abstract: A method and apparatus for fabricating an array of polynucleotides on a substrate. A polynucleotide deposition system is operated to deposit an array of polynucleotide containing fluid droplets on the substrate and which, when dry, will yield polynucleotide containing spots of respective target locations and dimensions. Droplets deposited by the system are allowed to dry to yield actual spots. An image is captured of the substrate with dried actual spots. Dried actual spot locations or dimensions from the image, are compared with target locations or dimensions of polynucleotide containing spots. A signal indicative of the result of the comparison may be generated.

Abstract: A method and apparatus for fabricating an array of polynucleotides on a substrate. A polynucleotide deposition system is operated to deposit an array of polynucleotide containing fluid droplets on the substrate and which, when dry, will yield polynucleotide containing spots of respective target locations and dimensions. Droplets deposited by the system are allowed to dry to yield actual spots. An image is captured of the substrate with dried actual spots. Dried actual spot locations or dimensions from the image, are compared with target locations or dimensions of polynucleotide containing spots. A signal indicative of the result of the comparison may be generated.

Abstract: A method and apparatus for fabricating an array of polynucleotides on a substrate. A polynucleotide deposition system is operated to deposit an array of polynucleotide containing fluid droplets on the substrate and which, when dry, will yield polynucleotide containing spots of respective target locations and dimensions. Droplets deposited by the system are allowed to dry to yield actual spots. An image is captured of the substrate with dried actual spots. Dried actual spot locations or dimensions from the image, are compared with target locations or dimensions of polynucleotide containing spots. A signal indicative of the result of the comparison may be generated.

Abstract: A method is described for removing residue from a fluid deposited on the interior surface of an inkjet printhead after the printhead has contained or dispensed the fluid at least once. The method makes use of a reverse flushing technique optionally used in combination with sonication. A cleaning station for flushing an inkjet printhead with a wash fluid, rinse fluid, and/or inert gas is provided as well.

Abstract: Methods are provided for depositing a quantity of fluid onto the surface of an array. In the subject methods, a thermal inkjet head loaded with the fluid is positioned in opposing relationship to, e.g. over, the array surface. Actuation of the thermal inkjet results in the expulsion of a quantity of fluid onto the array surface. The subject methods find particular use in array-based binding assays in which an array of binding agents is employed for the detection of an analyte(s), particularly array-based hybridization assays.

Abstract: Methods and devices for producing a biopolymeric array are provided. In the subject methods, an in situ approach is employed, where the subject methods are characterized by producing a first volume of fluid activator on a substrate surface and then depositing a second volume of a monomer onto the first volume, where the second volume is smaller than the first volume. Also provided are devices configured for use in the subject methods, including devices that provide for bi-directional array printing.

Abstract: An array unit comprising a substrate surface carrying multiple chemical arrays each comprising multiple features and each array being surrounded by a surface energy transition to maintain a separation between separate liquid samples applied to the arrays, and wherein the substrate surface is physically uninterrupted over a continuous region carrying the arrays. Methods of array fabrication and use are further provided.

Abstract: Methods of preparing biopolymeric arrays are provided. The subject methods include immobilizing at least a first population of a number of copies of a first probe for a first target to a surface of a solid support, wherein the number of probe copies of the first population is dependant on the at least suspected abundance of the target in a sample for which the array is designed. Also provided are biopolymeric arrays that include at least a first population of a number of copies of a first probe for a first target immobilized on a surface of a solid support, wherein the number of probe copies is dependant on the at least suspected abundance of the target present in a sample for which the array is designed to assay. The subject invention also includes algorithms present on computer readable mediums and kits for use in practicing the subject methods.

Abstract: A method, apparatus and computer program product, for fabricating an array of biopolymers on a substrate. The method uses a biopolymer or biomonomer fluid and a drop dispenser having a chamber into which the fluid is loaded and an orifice communicating with the chamber from which the fluid is dispensed. The method includes, when the chamber is loaded, applying a prime pressure to the fluid which varies over a range sufficient to move fluid within the drop dispenser but insufficient to cause fluid to be dispensed from the orifice. Drops are dispensed from the dispenser to the substrate so as to form the array.

Abstract: A method of fabricating an addressable array of biopolymer probes on a substrate according to a target array pattern using a deposition apparatus, and a deposition apparatus which can execute the method and computer program products for the apparatus. The deposition apparatus which, when operated according to a target drive pattern based on nominal operating parameters of the apparatus, provides the probes on the substrate in the target array pattern. The method includes examining at least one operating parameter for an error from a nominal value which error will result in use of the target drive pattern producing a discrepancy between the target array pattern and an actual array pattern deposited. When an error is detected deriving, based on the error, a corrected drive pattern different from the target drive pattern such that use of the corrected drive pattern results in a reduced discrepancy between the target and actual array patterns.

Abstract: Liquids are transferred from a plurality of wells or depots having openings arranged in a selected format to one or more receptacles, by displacing liquid contained in each well so that a convex meniscus swells from the opening, and contacting the receptacle with the swollen meniscus to draw a portion of the liquid into the receptacle. An apparatus for carrying out the method includes a depot member having a plurality of wells having openings supported in a selected format, and a receiving member defining at least one receptacle and usually a plurality of receptacles in a corresponding or complementary format; means for displacing liquid contained within the wells toward and through the openings; and means for bringing at least one selected well opening into proximity with at least one selected receptacle.

Abstract: Liquids are transferred from a plurality of wells or depots having openings arranged in a selected format to one or more receptacles, by displacing liquid contained in each well so that a convex meniscus swells from the opening, and contacting the receptacle with the swollen meniscus to draw a portion of the liquid into the receptacle. According to the invention, the liquid transfer is effected directly from the depot to the corresponding receptacle without contact between depots and receptacles, and without interposition of any transfer device between depots and receptacles.

Abstract: A method of fabricating an addressable array of chemical probes at respective feature locations on a substrate surface. The method may use a deposition apparatus with a substrate unit which includes the substrate and with a drop deposition unit which includes a drop deposition head. Such an apparatus when operated according to a target drive pattern based on nominal operating parameters of the apparatus provides the probes on the substrate surface in the target array pattern. The method may include depositing at least one drop from the head unit onto the substrate surface. A fiducial on the substrate unit is optionally viewed from a sensor. A deposited drop on the substrate surface is viewed from a sensor. An actual position of the viewed deposited drop may be determined relative to a fiducial on the substrate unit, based on the views of the fiducial and deposited drop. An error is determined based on any difference between the actual and target positions.

Abstract: A method of fabricating an array of different chemical moieties. The method may include ejecting drops containing the different moieties or precursors thereof from an orifice in an ejector head onto a substrate surface spaced from the orifice so as to form the array. The substrate surface may have structures adjacent each of multiple feature locations so as to assist in confining drops ejected onto the surface to the feature locations, which structures comprise channels or deposited raised members adhering to the surface and extending above adjacent feature locations. An array of different chemical moieties is also provided which has features at respective locations on a planar substrate surface having structures comprising channels or deposited raised barriers adhering to the surface, and which structures are adjacent each of multiple feature locations.

Abstract: Methods and apparatus for delivering a plurality of different biological materials onto discrete locations on a receiving surface, as for example to fabricate an array of different biological materials. The apparatus and methods may include a plurality of orifices in an orifice member, at least six delivery chambers each in fluid conducting relationship with at least one of the orifices, a plurality of reservoirs each in fluid communication with at least one of the delivery chambers, means associated with each orifice for propelling fluid through the associated orifice from the delivery chamber that is in fluid conducting relationship with the orifice, and a vent for commonly venting at least two of the reservoirs. In some embodiments the chambers and reservoirs are loaded with fluids containing selected biomolecules by drawing the selected fluids into the chambers through the orifices; in other embodiments the fluids are introduced into the reservoirs.

Abstract: Methods of performing array-based assays are provided. A feature of the subject methods is that a sample is initially contacted with a first substrate, i.e., a backing element, to produce a substrate supported sample. Next, the resultant substrate supported sample is contacted with an array of at least two different ligands, and the presence of any resultant surface bound binding complexes is detected. Also provided are backing elements, as well as kits and systems, for use in practicing the subject methods. The subject methods and compositions find use in any array based application, including genomic and proteomic applications.

Abstract: A multiple array substrate having multiple assay chambers, each assay chamber containing one or more arrays. The assay chambers include a form-in-place gasket between a substrate and a cover. Methods of forming such multiple array substrates are described. The assay chambers may further be associated with an analysis site for analyzing a sample solution contained within the assay chamber. Each assay chamber is in fluid communication with a port, and the ports are positioned in a spatial format adapted to interface to standard laboratory equipment for handling multiple fluids in parallel.