EQUIPMENT LIST & DESCRIPTIONS | Research Core

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 Invitrogen BigFoot Spectral Cell Sorter is a high-throughput sorter with 5 spatially separated lasers (349nm, 405nm, 488n, 561nm and 640nm) and 55 detectors.  The Bigfoot utilizes the newest technology of spectral flow cytometry, capturing the entire emission spectrum of each fluorophore rather than just the peak emission band. Sorting rates exceed 70,000 events per second, and sorting is configurable: from six-way sorting into tubes to multi-way sorting into 96-well or 384-well plates.  The sorter is housed in an integrated BSL-2 biosafety enclosure for optimal safety.

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 Leica Stellaris 8 STED is a high-end confocal microscope with an extended spectral range combined with STED (Stimulated Emission Depletion) super resolution system. The system is built on an inverted DMi8 CS Premium microscope base, with fully automated objectives, stage and filter turrets. The microscope is equipped with a 405 nm laser and a tunable (440 nm-790 nm) pulsed white-light laser for excitation and five Power HyD detectors. STED Super-Resolution microscopy system includes three pulsed STED lasers (589 nm, 660 nm, and 775 nm), and is able to achieve resolution of less than 50 nm in the lateral direction and 130 nm in the axial direction. 

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 Olympus FVMPE-RS Multiphoton System is purpose-built for deep imaging in biological tissue, aimed at revealing both detail and dynamics. It is an upright microscope with gantry frame, optimized for intravital imaging with a large space for live animals and experimental equipment. Innovative features for efficient delivery and detection of photons in scattering media enable high signal-to-noise ratio acquisition. The system is equipped with a dual wavelength laser with a tunable range from 680 nm to 1300 nm and a fixed wavelength line at 1045 nm (InSight X3 Dual-OL by Spectra-Physics). Hybrid scan unit consists of a high-speed acquisition resonant scanner and a high-definition galvanometer scanner. High-sensitivity GaAsP detectors and Olympus dedicated multiphoton objectives allow for deep tissue imaging under in vivo and cleared tissue conditions up to 8 mm deep

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 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 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.

The 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 Chromium X Series is a more flexible instrument that can partition cells for all single cell assays, including high-throughput assays.

The Visium CytAssist simplifies the Visium workflow by facilitating the transfer of transcriptomic analytes in human and mouse FFPE samples from standard glass slides to Visium slides.