Abstract: Methods for cell analysis are provided, comprising cell capturing, characterization, transport, and culture. In an exemplary method individual cells (and/or cellular units) are flowed into a microfluidic channel, the channel is partitioned into a plurality of contiguous segments, capturing at least one cell in at least one segment, A characteristic of one or more captured cells is determined and the cell(s) and combinations of cells are transported to specified cell holding chamber(s) based on the determined characteristic(s). Also provided are devices and systems for cell analysis.

Abstract: The invention relates to the use of inductively coupled plasma mass spectroscopy for cellular sample analysis. In some embodiments a method of performing mass spectroscopy analysis using an inductively coupled plasma mass spectroscopy system is provided. The method may include introducing a cellular sample comprising one or more cells or cellular particles into an inductively coupled plasma of the inductively coupled plasma mass spectroscopy system. The method may further include using the inductively coupled plasma mass spectroscopy system to assess the cellular sample by detecting and measuring one or more element tags in the cellular sample based on the element or isotopic compositions of the one or more element tags.

Abstract: Described herein are methods useful for incorporating one or more adaptors and/or nucleotide tag(s) and/or barcode nucleotide sequence(s) one, or typically more, target nucleotide sequences. In particular embodiments, nucleic acid fragments having adaptors, e.g., suitable for use in high-throughput DNA sequencing are generated. In other embodiments, information about a reaction mixture is encoded into a reaction product. Also described herein are methods and kits useful for amplifying one or more target nucleic acids in preparation for applications such as bidirectional nucleic acid sequencing. In particular embodiments, methods of the invention entail additionally carrying out bidirectional DNA sequencing. Also described herein are methods for encoding and detecting and/or quantifying alleles by primer extension.

Abstract: Apparatus and methods for delivering biological samples to an ICP source of a mass cytometer are disclosed. Biological material is disposed on a plurality of discrete sites on a carrier. The plurality of discrete sites are configured to retain biological material and to release the biological material upon application of energy. The carrier is positioned in proximity to a gas conduit and upon release from the discrete sites, the biological material becomes entrained in a gas flow, which delivers discrete portions of biological material through the conduit to the ICP source for analysis by mass cytometry. The apparatus and methods can provide a continuous stream of discrete portions of biological material to a mass cytometer or mass spectrometer.

Abstract: Analyzing samples injected into an inductively coupled plasma source can be improved by one or more of a stabilizing solution mixable with a sample prior to injection and a heated injector. The stabilizing solution can minimize the difference in osmotic pressure between the solution and the cells with a relatively low amount of dissolved solids (e.g., at or below about 0.2%). The stabilizing solution can contain a salt (e.g., ammonium nitrate) present in concentrations of at least 5 mM. The injector can be heated before and/or during injection. In some cases, heat from adjacent parts can be channeled into the injector to improve heating of the injector. An injector heated to sufficient temperatures can minimize solute buildup and can extend the usable time between cleanings. These improvements can be especially useful in elemental analysis, such as inductively coupled plasma mass spectrometry or inductively coupled plasma optical emission spectrometry.

Abstract: An analytical instrument has a sample introduction system for generating a stream of particles from a sample. An ionization system atomizes and ionizes particles in the stream as they are received. The instrument has an ion pretreatment system and a mass analyzer. The ion pretreatment system is adapted to transport ions generated by the ionization system to the mass analyzer. The mass analyzer is adapted measure the amount of at least one element in individual particles from the stream by performing mass analysis on the ions from the atomized particles. The instrument can be adapted to measure the amount of many different tags, for example at least five different tags, at the same time to facilitate multi-parametric analysis of cells and other particles.

Abstract: In certain embodiments, the present invention provides amplification methods in which nucleotide tag(s) and, optionally, a barcode nucleotide sequence are added to target nucleotide sequences. In other embodiments, the present invention provides a microfluidic device that includes a plurality of first input lines and a plurality of second input lines. The microfluidic device also includes a plurality of sets of first chambers and a plurality of sets of second chambers. Each set of first chambers is in fluid communication with one of the plurality of first input lines. Each set of second chambers is in fluid communication with one of the plurality of second input lines. The microfluidic device further includes a plurality of first pump elements in fluid communication with a first portion of the plurality of second input lines and a plurality of second pump elements in fluid communication with a second portion of the plurality of second input lines.

Abstract: An analytical instrument has a sample introduction system for generating a stream of particles from a sample. An ionization system atomizes and ionizes particles in the stream as they are received. The instrument has an ion pretreatment system and a mass analyzer. The ion pretreatment system is adapted to transport ions generated by the ionization system to the mass analyzer. The mass analyzer is adapted measure the amount of at least one element in individual particles from the stream by performing mass analysis on the ions from the atomized particles. The instrument can be adapted to measure the amount of many different tags, for example at least five different tags, at the same time to facilitate multi-parametric analysis of cells and other particles.

Abstract: Described herein are cell-based analytic methods, including a method of incorporating nucleic acid sequences into reaction products from a cell population, wherein the nucleic acid sequences are incorporated into the reaction products of each cell individually or in small groups of cells individually. Also described herein is a matrix-type microfluidic device that permits at least two reagents to be delivered separately to each cell or group of cells, as well as primer combinations useful in the method and device.

Abstract: A microfluidic system includes a substrate, a set of input ports coupled to the substrate, and a set of output ports coupled to the substrate. The microfluidic system also includes a microfluidic processing system coupled to the substrate and including a plurality of processing sites. The microfluidic processing system is coupled to the set of input ports and the set of output ports. The microfluidic system further includes one or more microfluidic logic devices coupled to the substrate and operable to control at least a portion of the microfluidic processing system.

Abstract: The invention relates to methods and devices for analysis of samples using laser ablation imaging mass cytometry and mass spectrometry. The invention provides methods and devices in which individual ablation plumes are distinctively captured and rapidly transferred to the ionization system, followed by analysis by mass spectrometry. A transfer conduit can be used to convey ablation plumes to an ionization system. The transfer conduit can include an asymmetric cone. The transfer conduit can be tapered. A flow sacrificing system can be adapted to divert a part of the sheath flow out a sacrificial outlet while the core of the sheath flow containing ablation plumes enters the ionization system.

Abstract: The invention relates to methods and devices for analysis of samples using laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). The invention provides methods and devices in which individual ablation plumes are distinctively captured and transferred to the ICP, followed by analysis by mass cytometry.

Abstract: Element tags based on novel metal-polymer conjugates are provided for elemental analysis of analytes, including ICP-MS. A polymer backbone is functionalized to irreversibly bind metals that are selected prior to use by the user. The polymer is further functionalized to attach a linker which allows for attachment to antibodies or other affinity reagents. The polymer format allows attachment of many copies of a given isotope, which linearly improves sensitivity. The metal-polymer conjugate tags enable multiplexed assay in two formats: bulk assay, where the average biomarker distribution in the sample is diagnostic, and single cell format to distinguish a rare (for example a diseased) cell in a complex sample (for example, blood).

Abstract: The present invention provides reagents, kits, and methods for single-cell whole genome amplification using Phi 29 DNA polymerase.

Abstract: A thermal cycler for a microfluidic device includes a controller operable to provide a series of electrical signals, a heat sink, and a heating element in thermal communication with the heat sink and operable to receive the series of electrical signals from the controller. The thermal cycler also includes a thermal chuck in thermal communication with the heating element. The thermal chuck comprises a heating surface operable to make thermal contact with the microfluidic device. The heating surface is characterized by a temperature ramp rate between 2.5 degrees Celsius per second and 5.5 degrees Celsius per second and a temperature difference between a first portion of the heating surface supporting a first portion of the microfluidic device and a second portion of the heating surface supporting a second portion of the microfluidic device is less than 0.25° C.

Abstract: Methods, reagents, and kits for detection and analysis of nucleic acids are provided. The methods can be used in conjunction with a proximity extension assay for protein detection to provide a multiplex assay to detect both nucleic acids (e.g., RNA) and proteins.

Abstract: Described herein are cell-based analytic methods, including a method of incorporating nucleic acid sequences into reaction products from a cell population, wherein the nucleic acid sequences are incorporated into the reaction products of each cell individually or in small groups of cells individually. Also described herein is a matrix-type microfluidic device that permits at least two reagents to be delivered separately to each cell or group of cells, as well as primer combinations useful in the method and device.

Abstract: A method for cellular analysis of cellular particles tagged with elemental tags, such as lanthanide-based elemental tags. Particles or element tags associated with particles can be vaporized, atomized, and ionized, such as with an inductively coupled plasma device or a glow discharge device. The vaporized, atomized, and ionized particles or element tags can be analyzed using mass spectrometry, such as using a time of flight mass spectrometer or a magnetic sector mass spectrometer. The amount of at least one element in individual particles can be measured through mass analysis. The amount of many different tags, for example at least five different tags, can be measured at the same time to facilitate multi-parametric analysis of cells and other particles. The vaporized, atomized, and ionized particles or element tags can be pretreated in an ion pretreatment system to filter out low mass ions, such as using a high-pass mass filter or a bandpass mass filter, to allow the elemental tags to pass therethrough.

Abstract: The inventors have improved mass cytometer to facilitate its use for the analysis of particles.

Abstract: A method for carrying out nucleic acid amplification reactions using a microfluidic device is described. Amplification primers and other amplification reagents are deposited at a plurality of reaction sites in the device, a sample solution containing amplifiable polynucleotides is introduced into the reaction sites, and amplification is carried out.