Abstract: An encoded microparticle carrying a spatial code is provided; and a set of encoded microparticles are provided with distinguishable spatial codes, wherein the codes comply with a pre-determined coding scheme. Presented are also methods of using the encoded microparticles in various biological assays, such as various multiplex quantitative PCR (real-time PCR) and multiplex chromosomal immunoprecipitation (ChIP) assays.

Abstract: Methods of detecting various types of nucleic acids, including methods of detecting two or more nucleic acids in multiplex branched-chain DNA assays, are provided. Detection assays may be conducted at least in vitro, in cellulo, and in situ. Nucleic acids which are optionally captured on a solid support are detected, for example, through cooperative hybridization events that result in specific association of a label probe system with the nucleic acids. Various label probe system embodiments are provided. Embodiments are directed to concurrent detection of one or more nucleic acids and one or more proteins. Embodiments also are directed to determining the methylation state of a target sequence. Other embodiments are directed to detection of one or more proteins using DNA barcodes. Compositions, kits, and systems related to the methods are also described.

Abstract: Methods of capturing two or more nucleic acids simultaneously from a single sample are provided. Different nucleic acids are captured through cooperative hybridization events on a substrate, or different subsets of particles, or at different selected positions on a spatially addressable solid support. Methods described include enrichment and purification of nucleic acids prior to downstream steps including sequencing of target nucleic acids. Compositions, kits, and systems related to the methods are also described.

Abstract: A method and apparatus of imaging fluorescence in situ hybridization (FISH) is provided. The instrument allows the user to simultaneously acquire images from several different colors. This system, used in conjunction with a combinatorial fluorescence approach, is able to create a FISH karyotype with each chromosome being painted with a different color. The optical system is continuously tunable over the detection wavelengths. In one embodiment of the system the sample is simultaneously irradiated in more than one wavelength band and the detection system uses a common path interferometer to scan through the detection wavelengths.

Abstract: A method and apparatus of imaging fluorescence in situ hybridization (FISH) is provided. The instrument allows the user to simultaneously acquire images from several different colors. This system, used in conjunction with a combinatorial fluorescence approach, is able to create a FISH karyotype with each chromosome being painted with a different color. The optical system is continuously tunable over the detection wavelengths. In one embodiment of the system the sample is simultaneously irradiated in more than one wavelength band and the detection system uses a common path interferometer to scan through the detection wavelengths.

Abstract: The invention relates to a method of identifying the individual autosomal and sex chromosomes of a human karyotype through the use of a set of combinatorially labeled oligonucleotide probes each member thereof: (i) having a predetermined label distinguishable from the label of any other member of said set, and (ii) being capable of specifically hybridizing with one predetermined autosomal or sex chromosome of a human karyotype.

Abstract: A method and apparatus of analyzing samples contained in a microplate is provided. The instrument is capable of measuring fluorescence, luminescence, and/or absorption within multiple locations within a sample well. The instrument is tunable over the excitation and/or detection wavelengths. Neutral density filters are used to extend the sensitivity range of the absorption measuring aspect of the instrument. Due to the wavelength tuning capabilities of the instrument, the spectral dependence of the measured fluorescence, luminescence, and absorption of the materials in question can be analyzed. The combination of a data processor and a look-up table improve the ease of operation of the instrument. Several different formats are available for the output data including creation of a bit map of the sample.

Abstract: A method and apparatus to detect fluorescence from a sample is provided. The optical system allows the user to continuously tune the wavelengths and bandwidths of the excitation source and the emission detection system. A peaking function automatically peaks the detected fluorescent signal by fine tuning the excitation and emission detection systems. A look-up table allows the fluorescent signal for a specific wavelength to be corrected for the wavelength dependence of the optical train. In one embodiment of the system the sample is simultaneously irradiated in more than one wavelength band, each wavelength band being independently tunable.

Abstract: This invention relates to a method of cloning DNA produced by primer extension including PCR amplified, reverse transcriptase-generated or primer extended synthetic DNA. Specifically, it relates to a method in which alkane diol residue containing oligonucleotide primers are incorporated into DNA by primer extension followed by direct cloning of the target DNA. Following transformation, the host excises the alkane diol residue with its endogenous DNA repair machinery.