Method for Detecting Transcription Factor-Protein Interactions
Granted: May 1, 2014
Application Number:
20140121122
A method is provided for identifying complexes between a transcription factor and another protein, the method comprising: isolating from a biological sample transcription factor complexes based on whether the transcription factor complexes comprise a particular type of transcription factor; and identifying which of a plurality of different proteins are present in the isolated transcription factor complexes.
Miniaturized microparticles
Granted: February 27, 2014
Application Number:
20140057809
A system and method for forming encoded microparticles is described. One embodiment includes an encoded microparticle, the microparticle comprising a plurality of segments aligned along an axis, wherein the plurality of segments define a code for the microparticle; and an outer cuboid encapsulating the plurality of segments, wherein the plurality of segments are detectable through the outer cuboid.
Multiple Step Printing Methods for Microbarcodes
Granted: February 20, 2014
Application Number:
20140051027
A system and method for forming encoded microparticles is described. One embodiment includes a method for forming a microparticle, the method comprising providing a pattern, wherein the pattern defines a code element, printing the pattern on a substrate to form a first code element within a microparticle region, printing the pattern on the substrate to form at least one successive code element, such that the first code element and the at least one successive code element are within the…
MANUFACTURING AND PROCESSING POLYMER ARRAYS
Granted: January 16, 2014
Application Number:
20140018266
The invention provides methods to process multiple microarrays by providing a microarray plate and processing plates. In an embodiment of the invention, methods for assembling microarray plates by using wafers are described for high throughput microarray processing.
Recombinant Colwellia Psychrerythraea Alkaline Phosphatase and Uses Thereof
Granted: December 26, 2013
Application Number:
20130344493
A heat labile alkaline phosphatase enzyme and methods of using the same and kits including the same are disclosed. Specifically, a nucleotide sequence of, peptide sequence of, methods of using, and kits comprising, a heat labile alkaline phosphatase isolated from Colwellia psychrerythraea are provided. Methods of over-expression and purification of the recombinant alkaline phosphatase and mutants thereof are also disclosed. Methods of over-expressing and purifying commercially useful…
Analysis of Data Obtained from Microarrays
Granted: September 5, 2013
Application Number:
20130230221
Disclosed are methods and software for biological data analysis. Specifically, provided are methods, computer programs and systems for analyzing data in the form of various intensity measurements obtained from an oligonucleotides microarray experiment. Such data may be microarray data obtained from an experiment conducted to determine copy number of a human genetic sample. The data are corrected by application of one or more covariate adjusters which may be applied simultaneously and…
Biological Assays Using Microparticles
Granted: August 15, 2013
Application Number:
20130210028
Encoded microparticles described are useful in the study of many different biological agents in multiplex assays. For instance, the encoded microparticles may be employed in various co-precipitation assays to purify and/or isolate various analytes of interest. Encoded microparticles may also be used as real-time detectors in many different situations whereby binding of a secreted analyte or contaminating analyte may be detected using various labeling techniques. Further, encoded…
Parallel Preparation of High Fidelity Probes in an Array Format
Granted: August 1, 2013
Application Number:
20130197208
The present invention provides massively parallel oligonucleotide synthesis and purification for applications that utilize large collections of defined high-fidelity oligonucleotides (e.g., from about 101 to about 105 different sequences, generally between 25-160 bases in length).
Methods of Analysis of Allelic Imbalance
Granted: July 25, 2013
Application Number:
20130190199
Methods are provided for identification of genes that are imprinted. In another embodiment methods are provided for identification and analysis of genes whose expression shows allelic imbalance. The expression products transcribed from genes that are present in the genome as two or more alleles may be distinguished by hybridization to an array designed to interrogate individual alleles. Genes whose transcription products are present in amounts that vary from expected are candidates for…
Microfluidic Methods, Devices, and Systems for Fluid Handling
Granted: July 25, 2013
Application Number:
20130190213
In one aspect of the invention, systems, methods, and devices are provided for handling liquid. In some embodiments, such systems, methods, and devices are used to process reagent biochemical reactions.
COMPUTER-AIDED VISUALIZATION OF EXPRESSION COMPARISON
Granted: July 4, 2013
Application Number:
20130169645
Innovative systems and methods for visualizing information collected from analyzing samples are provided. The samples may include nucleic acids, proteins, or other polymers. Gene expression level as determined from analysis of a nucleic acid sample is one possible analysis result that may be visualized. In one embodiment, a computer system may display the expression levels of multiple genes simultaneously in a way that facilitates user identification of genes whose expression is…
SURFACE LINKERS FOR ARRAY SYNTHESIS
Granted: June 27, 2013
Application Number:
20130165350
The present invention provide several methods of derivatizing a surface of a support with one or more linkers thus providing a suitable platform for synthesis of a polymer array, particular a nucleic acid array. Some methods derivatize a surface with a self-assembled monolayer (SAM) of a linker. The SAM confers advantages of hydrolytic stability, broad compatibility with synthesis and detection chemistries, and reduced emergence of latent functional groups during polymer array synthesis.…
Arrays of Nucleic Acid Probes for Analyzing Biotransformation Genes
Granted: June 13, 2013
Application Number:
20130150248
The invention provides arrays of immobilized probes, and methods employing the arrays, for detecting mutations in the biotransformation genes, such as cytochromes P450. For example, one such array comprises four probe sets. A first probe set comprises a plurality of probes, each probe comprising a segment of at least three nucleotides exactly complementary to a subsequence of a reference sequence from a biotransformation gene, the segment including at least one interrogation position…
Feature Intensity Reconstruction of Biological Probe Array
Granted: June 6, 2013
Application Number:
20130142408
The invention provides methods and systems for reconstructing feature intensities from pixel level data. In certain embodiments, the invention uses an empirically determined transfer function to construct a theoretical estimate of pixel level data and then iteratively updates feature intensities based on a minimum multiplicative error between the pixel level data and the theoretical estimate of the pixel level data.
Complexity Management of Genomic DNA
Granted: May 30, 2013
Application Number:
20130137583
The presently claimed invention provides for novel methods and kits for analyzing a collection of target sequences in a nucleic acid sample. A sample is amplified under conditions that enrich for a subset of fragments that includes a collection of target sequences. The invention further provides for analysis of the above sample by hybridization to an array, which may be specifically designed to interrogate the collection of target sequences for particular characteristics, such as, for…
Methods, Systems and Apparatuses for Testing and Calibrating Fluorescent Scanners
Granted: May 23, 2013
Application Number:
20130126757
Disclosed are calibration apparatuses for fluorescent microscopy instruments and methods of making and using them. Specifically, disclosed are calibration apparatuses with a fluorescent layer, such as photoresist, deposited on a substrate, with an optional layer of a reflective material, such as chrome. Illumination of the fluorescent and/or reflective layers, and detection and analysis of the resulting emissions allows evaluation of the instrument with respect to both reflective and…
Digital Counting of Individual Molecules by Stochastic Attachment of Diverse Label-Tags
Granted: May 9, 2013
Application Number:
20130116130
Compositions, methods and kits are disclosed for high-sensitivity counting of individual molecules by stochastic labeling of a identical molecules in mixtures of molecules by attachment of a unique label-tags from a diverse pool of label tags to confer uniqueness to otherwise identical or indistinguishable events. Individual occurrences of target molecules randomly choose from a non-depleting reservoir of diverse label-tags. Labeled molecules may be detected by hybridization or…
Maltoside and Phosphocholine Derivatives, Uses thereof and Methods of Preparing Artificial Lipid Structures Thereof
Granted: April 18, 2013
Application Number:
20130096295
Disclosed are saccharide and phosphocholine derivatives. The derivatives include azide and alkyne derivatives which form one end of a variable length carbon chain. The opposite end of the variable length carbon chain is covalently linked to the saccharide or phosphocholine. The saccharide may be, for instance, a maltoside. The alkyne and azide derivatives of the saccharides and phosphocholine may be reacted together to form amphiphilic molecules useful in cellular membrane studies and…
Methods for Synthesizing Pools of Probes
Granted: March 21, 2013
Application Number:
20130072390
Compositions, methods and kits are disclosed for synthesizing and amplifying pools of probes using precursor oligonucleotides. In some aspects the precursor is amplified and nicking enzymes are used to separate the full length probes from the amplification products. The methods enable the preparation of single stranded DNA probes of defined sequence and length that are suitable for use in target detection assays.
System for photolithographic synthesis of polymer arrays
Granted: March 7, 2013
Application Number:
20130059763
The present invention provides novel processes for the large scale preparation of arrays of polymer sequences wherein each array includes a plurality of different, positionally distinct polymer sequences having known monomer sequences. The methods of the invention combine high throughput process steps with high resolution photolithographic techniques in the manufacture of polymer arrays.
