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.

ACEA NovoCyte Quanteon
The ACEA NovoCyte Quanteon analyzer is a 4-laser flow cytometer capable of detecting up to 27 parameters (forward scatter, side scatter, and 25 fluorescence detectors).  In addition to a 405nm, 488n, and 637nm laser, it includes a 561nm laser, which provides the ability to excite yellow and green fluorophores of conjugated antibodies.  

BD Biosciences FACSAriaIII
The 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. It is capable of standard “bulk” sorting of up to four user-defined cell populations simultaneously, or can be used for direct deposition of a counted number of cells directly 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.

BD Biosciences LSRII-SORP
This BD LSRII is capable of detecting up to 17 parameters (Forward Scatter, Side Scatter, and fifteen 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 performs laser capture microdissection from heterogeneous tissue samples simply, quickly, and precisely. In minutes the investigator can locate a single cell or large groups of cells and, using a simple aim-and-shoot method, extract them for subsequent molecular analysis. LCM preserves the exact morphologies of both the captured cells and the surrounding tissue. The Arcturus XT transfers cells from paraffin-embedded and frozen tissue sample stained slides. The entire process can be monitored and documented, and the images stored in an archiving workstation.  Research applications include genomics (differential gene profiling, loss of heterozygosity, microsatellite instability, and gene quantification) and proteomics (two-dimensional protein gels, Western blotting, and immuno-quantification of proteins). 

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 Research Core Facility is equipped with a state-of-the-art Affymetrix GeneChip System that allows whole genome expression analysis for a wide variety of organisms.  The Affymetrix GeneChip System consists of the following components:

1. A GeneChip Hybridization Oven 645 for automated control of hybridization to the GeneChip arrays.
2. A GeneChip Fluidics Station 450 for automated washing of arrays and labeling of hybridized probes. This station can wash and stain four arrays simultaneously.
3. A GeneChip Scanner 3000 7G with Autoloader for obtaining high-resolution images of hybridization signals.
4. A GeneChip Workstation that controls the operation of the system, data collection and processing of initial raw data.
5. A bioinformatics system including  Transcriptome Analysis Console, and Ingenuity Pathway Analysis.

Leica TCS SP5 Confocal Microscope
This 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 newest version of LAS AF software (LAS AF 2.6.3), with FRAP, FRET, Mark & Find, 3D Visualization, Colocalization, and Live Data Modes.

Nikon A1R Confocal & SIM Super Resolution System
This is a high-speed Nikon A1R 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. 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 CO2, O2, and humidity controls.

Nikon Widefield Microscope
The system is built around a Nikon Eclipse TE300 inverted microscope with a range of objectives for phase, DIC, and high resolution epifluorescent imaging. The software package controls a Prior OptiscanTM XYZ stage with a full complement of stage inserts and a Prior filter wheel containing excitation filters from the Chroma 83000 filter set. This set includes single and multiband excitation filters for DAPI, FITC, GFP, Texas Red, Rhodamine, or PI. Fluorescent images are acquired with a black and white ANDOR Neo/Zyla camera; high resolution color images may also be acquired with the DS Fi2 color camera. The stage, filters, shutters, and camera are controlled by the NIS Elements software from Nikon.

Olympus iXplore CSU W1 Spinning Disk
This 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 microscope is equipped with two cutting-edge sCMOS cameras (Hamamatsu Fusion) for simultaneous acquisition on two channels. The Yokogawa CSU W1 spinning disk unit houses two disks (25  and 50 µm ) to best fit different objectives. The system is connect to a feedback stage-top incubation chamber for CO₂, and humidity control.  A recently added VAHEAT precise temperature control unit allows for fast and precise temperature adjustments, making it ideal for heat-shock studies.

Zeiss AxioObserver/Apotome Microscope 
The 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.

Zeiss LSM 510 NLO Confocal/Multiphoton Microscope
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.

Off-line Image Analysis Stations There are two computer stations in the Core Facility Computer Lab reserved for microscope users, which are loaded with specialized imaging software. The RCFoffline2 system (Fujitsu/Siemens Celsius R650) has two processors, four terabyte hard drives, and an ATI Fire GL V7350 video card with 1 GB of on-board memory. It runs on Windows XP Professional (32 bit) and is loaded with 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. RCFoffline1, a Dell Optiplex 3010, runs on Windows 7 Professional (64 bit) and is loaded with Leica LAS AF 2.6.3, NIS Elements  AR 4.13.04, and Zeiss LSM 510 ZEN 2009.

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

Cluster generation, sequencing and analysis are all performed on the MiSeq. The sequencing process takes place on a single channel flow cell. Multiple samples can be pooled together and sequenced by using unique index barcodes during library preparation

Illumina NextSeq 550 Next Generation Sequencer
The NextSeq 550 is a more flexible system, enabling the analysis of transcriptomes and whole exams. It is capable of generating up to 120 Gb of output with up to 400 M single sequencing reads and up to 2 x 150 bp read lengths.  The NextSeq 550 also includes the capability of scanning cytogenomic BeadChip arrays.

Illumina NovaSeq 6000 Next Generation Sequencer
The NovaSeq 6000 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 is capable of generating up to 10 B single-end sequencing reads. It combines two-color chemistry along with patterned flow cell technology.  

10X Genomics Chromium Controller
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.  

Bio-Rad CFX96 Fast Touch Real-Time PCR Systems
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. 

Bio-Rad CFX384 Touch Real-Time PCR System
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) provide precise quantification and multiplex target discrimination.  All other acquisition and analysis parameters are identical to the CFX96 Fast System.