The Agilent Seahorse XFe24 Analyzer measures the oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) of live cells in a 24-well plate format.  OCR and ECAR rates are key indicators of mitochondrial respiration and glycolysis, as well as ATP production rate, and together these measurements provide a systems-level view of cellular metabolic function in cultured cells and ex-vivo samples.

The ACEA NovoCyte Quanteon analyzer is a 4-laser (405nm, 488nm, 561nm, & 637nm) flow cytometer capable of detecting up to 27 parameters (forward scatter, side scatter, and 25 fluorescence detectors).  The silicon photomultipliers (SiPM) provide stable 7.2 log dynamic range. Multiple input sources (5mL tubes, 96 and 384 well plates) make sample acquisition extremely flexible.  Data can be directly transferred into an Excel spreadsheet, ensuring ease of data analysis.

The BD FACSAriaIII cell sorter is capable of 17-parameter (forward scatter, side scatter, and 15 fluorescence detectors) analysis and cell sorting. It has four solid-state lasers for excitation at wavelengths of 405 nm, 488 nm, 561 nm and 633 nm. It is a digital high-speed sorter, capable of sorting up to 70,000 events per second and standard “bulk” sorting of up to four user-defined cell populations simultaneously.  It can also be used for direct deposition of a counted number of cells into tissue culture plates for cloning, frequency response assays, or other single cell analyses. This instrument uses BD Biosciences FacsDiva software for acquisition and analysis.

The BD LSRII-SORP is capable of detecting up to 17 parameters (forward scatter, side scatter, and 15 fluorescence detectors).  It has four solid-state lasers for excitation at wavelengths of 405 nm, 488 nm, 561 nm and 633 nm.  This instrument uses BD Biosciences FacsDiva software for acquisition and analysis.

The Arcturus XT Laser Capture Microdissection System offers an automated approach to the microdissection of isolated cells or multicellular structures from FFPE or frozen tissue slides. This technique preserves the exact morphologies of both the captured cells and the surrounding tissue.  Specifically developed caps coated with a thermoplastic film are placed on the region of interest.  The Arcturus XT instrument is then used to direct a low-powered infrared laser through the cap to melt the film onto the cells of interest.  These cells adhere to the cap when it is lifted from the tissue section, thus capturing them for further analysis.  The laser does not affect the tissue sample; therefore, the quality of the nucleic acids and proteins within the sample is not compromised. 

The Thermo Scientific™ Orbitrap Exploris™ 480 Mass Spectrometer is a quadrupole-Orbitrap™ mass spectrometer which provides high-resolution, accurate-mass (HRAM) data, generating incredibly high resolution measurements of up to 480,000 FWHM at m/z 200.  Due to its HRAM capabilities, it can be used for low-abundance, high complexity samples at sub-ppb concentrations and /or sub-ppm mass differences. With the option to extend the mass range up to m/z 8000, it facilitates our in-depth characterization needs from intact, top and middle-down through to peptide mapping.

In addition, it is combined with Thermo Scientific™ UltiMate™ 3000 RSLCnano System and HPG-3200RS PUMP, which has a wide flow-pressure footprint with nano-, capillary-, micro-, and regular-flow options.

The Affymetrix GeneChip System is a commercial microarray platform that allows whole genome gene expression analysis for a wide variety of experimental organisms.  This system has four major advantages: it is inexpensive to use; it generates results quickly; it has the capability to monitor the expression of every gene in the genome; and it is the most widely used commercial microarray platform.  The Affymetrix GeneChip System consists of a GeneChip Hybridization Oven 645 for automated control of hybridization to the GeneChip arrays, a GeneChip Fluidics Station 450 for automated washing of arrays and labeling of hybridized probes, a GeneChip Scanner 3000 7G with Autoloader for obtaining high-resolution images of hybridization signals, a GeneChip Workstation that controls the operation of the system, data collection and processing of initial raw data, and a bioinformatics system including Transcriptome Analysis Console software.

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The Leica TCS SP5 Confocal Microscope is a very flexible and fast confocal system for fixed or living samples. The system includes a Leica DMI 6000 CS fully automated inverted microscope with motorized stage, condenser, objective, and filter turrets. The microscope is housed in a Ludin full enclosure incubator with an internal Ludin Cube2 with CO2, O2, and humidity controls. It is equipped with 5 lasers for excitation: violet diode (405 nm), multi-line Argon (458, 476, 488, 496, and 514 nm), green HeNe (543 nm), orange HeNe (594 nm), and red HeNe (633 nm); visualization is done using a mercury arc lamp. The spectral beam splitter has freely adjustable bandwidths for the collection of signal in 5 separate detectors simultaneously or sequentially. There is also a transmitted light detector for DIC. There are 9 available objectives, ranging from a 2.5x to a Plan Apo 100x/1.46 NA oil objective. The system runs on the LAS AF software (LAS AF 2.6.3), with FRAP, FRET, Mark & Find, 3D Visualization, Colocalization, and Live Data Modes.

The Nikon A1R Confocal & SIM Super Resolution System is a high-speed confocal microscope combined with a SIM (Structured Illumination Microscopy) super resolution system for fixed and live sample-imaging. The Nikon Eclipse Ti-E inverted microscope is built with fully automated objectives, stage, and filter turrets. The 5 objectives range from 10X to 100X. The confocal components include 5 detectors and 4 lasers: 405nm, 488nm, 561nm, and 640nm in wavelength. The SIM components include a Hamamatsu camera and 3 LED lasers: 488nm, 561nm, and 640nm in wavelength and CFI SR HP APO TIRF 100XC NA 1.49 OIL W objective. DAPI images can still be taken under SIM mode. The microscope is capable for bright-field imaging, multichannel fluorescence imaging, large image stitching, multipoint acquisition, time-lapse acquisition, FRAP, FRET imaging, and 2D/3D deconvolution. The resolution for conventional confocal reaches 200-250nm, while the resolution for super resolution system reaches 85-100nm. To allow long hour live cell-imaging, the microscope is housed in an incubator with temperature, CO2, and humidity controls (Tokai Hit controller).

The Olympus iXplore SpinSR is a high-resolution and fast spinning disk confocal system built on an inverted IX83 microscope base, with fully automated objectives, stage, and filter turrets. The confocal components include 4 lasers: 405nm, 488nm, 561nm, and 640nm in wavelength. The microscope is equipped with two cutting-edge sCMOS cameras (Hamamatsu ORCA-Fusion Gen -III) for simultaneous acquisition in two channels. The Yokogawa CSU W1 spinning disk unit houses two disks (25 and 50 µm) to best fit different objectives (range from 10X to 100X). The system is also equipped with a feedback stage-top incubation WSKMX chamber for temperature, CO2, and humidity control (Tokai Hit controller). 

The Zeiss AxioObserver/Apotome system is built around a Zeiss AxioObserver Z1 inverted fluorescent microscope, fully automated, with component recognition to minimize errors. System components include mercury arc lamp excitation, a Zeiss AxioCamMRm CCD camera with 12-bit dynamic range, extended sensitivity in the near infrared, a fully automated XYZ stage, a complement of objectives ranging from 10x to 100x, and five installed filter sets for DAPI, FITC, narrow band GFP, Rhodamine, and Far Red. The Apotome attachment is designed for precise optical sectioning. The Apotome slides easily into the optical path and projects a grid onto the image plane, which is shifted laterally in three defined steps, with an image collected at each step. A software algorithm then removes any out-of-focus signal. The acquisition software is AxioVision v.4.8, including plug-in options for Inside 4D, 3D Deconvolution, Colocalization, Mark & Find, Mosaic, and more.

The Zeiss LSM 510 NLO system is configured to enhance living tissue research. The scanning system is connected to an upright Axioskop 2 FS MOT microscope equipped with a set of objectives selected for physiological measurements and live animal studies. The stage remains in a fixed position, and the objectives have motorized focus control. It is equipped with the following lasers and laser lines for excitation: Argon (458, 477, 488, 514 nm), HeNe (543 nm), HeNe (633 nm), and the Coherent Chameleon-XR Ti: Sapphire laser (tunable from 705 to 980 nm). The ultrafast-pulsed Chameleon laser emitting NIR radiation allows imaging up to 500 μm deep within tissue. There are three PMTs for visible wavelength detection, a transmitted light detector, and two non-descanned detectors for multiphoton imaging. The LSM 510 ZEN operating software includes the Physiology v3.5 and Image Visart v3.5 options that permit 2D, 3D, and 4D image collection and processing, 3D/4D animation, calibration and measurement of ion concentrations, time series analysis, and graphical mean-of-ROI analysis.

The Interherence VAHEAT is a precise temperature control unit for optical microscopes.  It combines local heating with direct temperature sensing, allowing for fast and precise temperature adjustment.  It is capable of heating rates up to 100°C/s while maintaining the highest temperature precision.  Sample is prepared on a smart substrate equipped with a transparent heating element and a precise temperature probe.  This unit is not specific to any one microscope and can be adapted for most. 

There are four computer stations in the Core Facility Computer Lab reserved for microscope users, which are loaded with specialized imaging software. 

• RCF offline1 - Leica LAS AF 2.6.3, NIS Elements AR 4.13.04, and Zeiss LSM 510 ZEN 2009.
• RCF offline2 - Media Cybernetics’ AutoQuant AutoDeblur deconvolution software (AutoQuant X3), including the AutoVisualize option, and full off-line versions of Zeiss LSM 510 AIM (confocal) and Zeiss Axiovision 4.8.2 (AxioObserver with Apotome) software.
• RCF offline3 - Bitplane Imaris 9.8 Single Full with Clearview software (MeasurementPro, ImarisTrackLineage, ImarisColoc, ImarisXT, ImarisCell, ImarisVantage, and ClearView-GPU™ Deconvolution). The package includes advanced functionality to detect cells and their major compartments, discover intracellular relationships, study motion, explore cell differentiation using an interactive lineage tree.
• RCF offilne4 - Bitplane Imaris 9.8 Satellite (see above), Olympus cellSens Dimension V2 (Multi-Position Solution, Count & Measure Solution, TruSight 3D Deconvolution Solution).

The Illumina MiSeq Next Generation Sequencer is most suited for focused applications such as small genome sequencing, metagenomics, amplicon sequencing and targeted gene sequencing. It can generate up to 15 GB of output with 25 M sequencing reads and up to 2 x 300 bp read lengths.

The Illumina NextSeq 550 Next Generation Sequencer is a more flexible system, enabling the analysis of targeted panels, transcriptomes, and whole exomes. It can generate up to 120 Gb of output with up to 400 M single sequencing reads and up to 2 x 150 bp read lengths.  

The Illumina NovaSeq 6000 Next Generation Sequencer offers the highest output and the lowest per base sequencing cost, making it ideal for applications requiring greater sequencing depth, such as single-cell RNA-Seq.  It supports read lengths of up to 2 x 250 bp and can generate up to 10 billion single-end sequencing reads. It combines two-color chemistry along with patterned flow cell technology.  

The 10X Genomics Chromium Controller performs single cell partitioning and barcoding, enabling integrated analysis of single cells on a massive scale, making it optimal for a number of sequencing applications, including single-cell RNA-Seq.  

The 10X Genomics Chromium Connect enables automatic 10X Genomics library construction for single cell gene expression and immune profiling applications.  10X Genomics library preparation is time consuming, and automating this task allows for increased throughput.

The Research Core Facility has three Bio-Rad CFX96 Fast Real-Time PCR Systems. The CFX96 is a six-channel real-time PCR system that combines advanced optical technology with precise thermal control to deliver sensitive, reliable detection. The system’s solid-state optical technology (six filtered LEDs, each with a corresponding filtered photodiode) maximizes fluorescence detection for specific dyes in specific channels, providing sensitive detection for quantitation and target discrimination. Data is collected from all wells during data acquisition. At every position and with every scan, the optics shuttle is reproducibly centered above each well, so the light path is always optimal and there is no need to sacrifice data collection on one of the channels to normalize to a passive reference. Users can select multiple data acquisition modes, including a one-color fast scan for SYBR green. Thermal gradient features can be used to optimize reactions in a single run. The new CFX Maestro software has advanced analysis tools for performing normalized gene expression. 

The Research Core Facility has one Bio-Rad CFX384 Touch Real-Time PCR System.  The system's solid-state optical technology (5 filtered LEDs and 5 filtered photodiodes) provides precise quantification and multiplex target discrimination.  All other acquisition and analysis parameters are identical to the CFX96 Fast System.