Abstract: In some embodiments, the disclosure relates generally to compositions, comprising a single reaction mixture containing a plurality of different populations of discrete supports, and a plurality of different populations of target nucleic acids. The single reaction mixture can contain a first population of beads; a second population of beads; a first population of target nucleic acids, where at least two different target nucleic acids in the first population of target nucleic acids can bind to a bead in the first population of beads; and a second population of target nucleic acids, where at least two different target nucleic acids in the second population of target nucleic acids can bind to a bead in the second population of beads. The single reaction mixture can be employed to monoclonally amplify the first target nucleic acids on the first beads, and monoclonally amplify the second target nucleic acids on the second beads.

Abstract: Energy transfer dye pairs including a donor dye covalently attached to an acceptor dye through a linker, uses of the energy transfer dye pairs, for example, in conjugates of an energy transfer dye pair covalently attached to a quencher and an analyte (e.g., an oligonucleotide), for biological applications including, for example, amplification assays such as quantitative polymerase chain reaction (qPCR) and digital PCR (dPCR).

Abstract: In some embodiments, the disclosure relates generally to compositions, comprising a single reaction mixture containing a plurality of different populations of discrete supports, and a plurality of different populations of target nucleic acids. The single reaction mixture can contain a first population of beads; a second population of beads; a first population of target nucleic acids, where at least two different target nucleic acids in the first population of target nucleic acids can bind to a bead in the first population of beads; and a second population of target nucleic acids, where at least two different target nucleic acids in the second population of target nucleic acids can bind to a bead in the second population of beads. The single reaction mixture can be employed to monoclonally amplify the first target nucleic acids on the first beads, and monoclonally amplify the second target nucleic acids on the second beads.

Abstract: A system (1000) comprising first and second excitation sources (101a, 101b) with respective excitation wavelengths for exciting first second and third dyes in a sample (110) and further comprising a detector (115), first and second emission spectral elements (121a, 121b) for transmitting respective first and second emission wavelengths as well as a processor (130) for automatically operating the elements of the system. The first dye comprises a first absorption spectrum comprising a first maximum absorption wavelength and the second dye comprises a second absorption spectrum comprising a second maximum absorption wavelength that is equal to or substantially equal to the first maximum absorption wavelength. The second dye comprises a second emission spectrum comprising a second maximum emission wavelength and the third dye comprises a third emission spectrum comprising a third maximum emission wavelength that is equal to or substantially equal to the second maximum emission wavelength.

Abstract: Energy transfer dye pairs including a donor dye covalently attached to an acceptor dye through a linker, uses of the energy transfer dye pairs, for example, in conjugates of an energy transfer dye pair covalently attached to a quencher and an analyte (e.g., an oligonucleotide), for biological applications including, for example, amplification assays such as quantitative polymerase chain reaction (qPCR) and digital polymerase chain reaction (dPCR). Systems and methods include those in which (1) two dyes have the same excitation wavelength range, but different emission wavelength ranges and/or (2) two dyes have the same emission wavelength range, but different excitation wavelength ranges.

Abstract: The present disclosure relates to N-protected NH-rhodamine dyes and their use in nucleic acid detection. In particular, the disclosure relates to methods of making N-protected NH-rhodamine dyes, and methods of use of N-protected NH-rhodamine dyes (e.g., human identification). Certain dyes provided herein have unique spectral properties that complement those in existing dye sets and can be used to expand the number of reporter dyes that can be included for HID applications and other biological assays. Those fluorescent compounds are useful to label synthetic oligonucleotides. Formula (I).

Abstract: The present invention is directed to fluorescent rhodamine dyes having spectral properties suited to the creation of multiplex assay systems for use in molecular biology, cell biology and molecular genetics.

Abstract: Silicon-substituted rhodamine compounds are disclosed herein. Also described herein are SiR dyes comprising at least one vinyl group attached to the Si atom (10 position) of the SiR dye. Derivatives, functionalized versions, conjugates, kits, related synthetic methods and uses of SiR compounds also are provided. Silicon-rhodamine (SiR) dyes can provide bright fluorescence at far red wavelengths and exhibit good photostability. The compounds described herein can be useful for fluorescent labeling and detection of biological samples.

Abstract: In some embodiments, the disclosure relates generally to compositions, comprising a single reaction mixture containing a plurality of different populations of discrete supports, and a plurality of different populations of target nucleic acids. The single reaction mixture can contain a first population of beads; a second population of beads; a first population of target nucleic acids, where at least two different target nucleic acids in the first population of target nucleic acids can bind to a bead in the first population of beads; and a second population of target nucleic acids, where at least two different target nucleic acids in the second population of target nucleic acids can bind to a bead in the second population of beads. The single reaction mixture can be employed to monoclonally amplify the first target nucleic acids on the first beads, and monoclonally amplify the second target nucleic acids on the second beads.

Abstract: Computing resources 202, from a cloud computing network 200, are adjusted for a virtualized operation. Data comporting to the computing sources 202 and metrics of the virtualized operation are received and compared against the parameters that are associated with the virtualized operation. When the data and metrics fall outside of the parameters, the virtualized operation and the computing resources 202 can be adjusted to make the use of cloud computing system 200 and resources be used more efficiently.

Abstract: The present teachings generally relate to fluorescent dyes, linkable forms of fluorescent dyes, energy transfer dyes, reagents labeled with fluorescent dyes and uses thereof.

Abstract: In some embodiments, the disclosure relates generally to compositions, comprising a single reaction mixture containing a plurality of different populations of discrete supports, and a plurality of different populations of target nucleic acids. The single reaction mixture can contain a first population of beads; a second population of beads; a first population of target nucleic acids, where at least two different target nucleic acids in the first population of target nucleic acids can bind to a bead in the first population of beads; and a second population of target nucleic acids, where at least two different target nucleic acids in the second population of target nucleic acids can bind to a bead in the second population of beads. The single reaction mixture can be employed to monoclonally amplify the first target nucleic acids on the first beads, and monoclonally amplify the second target nucleic acids on the second beads.

Abstract: Fluorescent phenyl xanthene dyes are described that comprise any fluorescein, rhodamine or rhodol comprising a particular C9 phenyl ring. One or both of the ortho groups on the lower C9 phenyl ring is ortho substituted with a group selected from alkyl, heteroalkyl, alkoxy, halo, haloalkyl, amino, mercapto, alkylthio, cyano, isocyano, cyanato, mercaptocyanato, nitroso, nitro, azido, sulfeno, sulfinyl, and sulfino. In one embodiment, halo and/or hydroxy groups are used. Optimal dyes contain a lower C9 phenyl ring in which both ortho groups are the same and the lower ring exhibits some form a symmetry relative to an imaginary axis running from the phenyl rings point of attachment to the remainder of the xanthene dye through a point para to the point of attachment. The phenyl xanthene dyes may be activated. Furthermore, the phenyl xanthene dyes may be conjugated to one or more substances including other dyes.

Abstract: A method of manufacturing a sensor, the method including forming an array of chemically-sensitive field effect transistors (chemFETs), depositing a dielectric layer over the chemFETs in the array, depositing a protective layer over the dielectric layer, etching the dielectric layer and the protective layer to form cavities corresponding to sensing surfaces of the chemFETs, and removing the protective layer. The method further includes, etching the dielectric layer and the protective layer together to form cavities corresponding to sensing surfaces of the chemFETs. The protective layer is at least one of a polymer, photoresist material, noble metal, copper oxide, and zinc oxide. The protective layer is removed using at least one of sodium hydroxide, organic solvent, aqua regia, ammonium carbonate, hydrochloric acid, acetic acid, and phosphoric acid.

Abstract: Fluorescent polymeric materials are disclosed comprising a polymer and one or more lipid soluble rhodamine dyes with the following core structure: The materials are especially useful in the preparation of multicolored microparticles, especially multicolored polystyrene microparticles, for use in the multiplexed analysis of a plurality of analytes in a single sample. When excited by a light source, the materials give off a unique emission based on the nature, concentration and ratio of the dyes therein. Methods of preparing and using the fluorescent polymeric materials are also disclosed.

Abstract: The present teachings generally relate to fluorescent dyes, linkable forms of fluorescent dyes, energy transfer dyes, reagents labeled with fluorescent dyes and uses thereof.

Abstract: Fluorescent phenyl xanthene dyes are described that comprise any fluorescein, rhodamine or rhodol comprising a particular C9 phenyl ring. One or both of the ortho groups on the lower C9 phenyl ring is ortho substituted with a group selected from alkyl, heteroalkyl, alkoxy, halo, haloalkyl, amino, mercapto, alkylthio, cyano, isocyano, cyanato, mercaptocyanato, nitroso, nitro, azido, sulfeno, sulfinyl, and sulfino. In one embodiment, halo and/or hydroxy groups are used. Optimal dyes contain a lower C9 phenyl ring in which both ortho groups are the same and the lower ring exhibits some form a symmetry relative to an imaginary axis running from the phenyl rings point of attachment to the remainder of the xanthene dye through a point para to the point of attachment. The phenyl xanthene dyes may be activated. Furthermore, the phenyl xanthene dyes may be conjugated to one or more substances including other dyes.

Abstract: A method of manufacturing a sensor, the method including forming an array of chemically-sensitive field effect transistors (chemFETs), depositing a dielectric layer over the chemFETs in the array, depositing a protective layer over the dielectric layer, etching the dielectric layer and the protective layer to form cavities corresponding to sensing surfaces of the chemFETs, and removing the protective layer. The method further includes, etching the dielectric layer and the protective layer together to form cavities corresponding to sensing surfaces of the chemFETs. The protective layer is at least one of a polymer, photoresist material, noble metal, copper oxide, and zinc oxide. The protective layer is removed using at least one of sodium hydroxide, organic solvent, aqua regia, ammonium carbonate, hydrochloric acid, acetic acid, and phosphoric acid.

Abstract: Extended rhodamine compounds exhibiting favorable fluorescence characteristics having the structure are disclosed. In addition, novel intermediates for synthesis of these dyes are disclosed, such intermediates having the structure In addition, methods of making and using the dyes as fluorescent labels are disclosed.

Abstract: Fluorescent polymeric materials are disclosed comprising a polymer and one or more lipid soluble rhodamine dyes. The materials are especially useful in the preparation of multicolored microparticles, especially multicolored polystyrene microparticle, for use in the multiplexed analysis of a plurality of analytes in a single sample. When excited by a light source, the materials give off a unique emission based on the nature, concentration and ratio of the dyes therein. Methods of preparing and using said materials are also disclosed.