EQUIPMENT
Agilent 2100 Bioanalyzer is a microfluidics-based platform for sizing, quantification and quality control of DNA, RNA, proteins and cells. This Lab-on-a-Chip technology utilizes a network of channels and wells that are etched onto a glass or polymer chip. Pressure or electrokinetic forces move pico-liter volumes in a finely controlled manner through the channels. The main advantages of Lab-on-a-Chip are ease-of-use, speed of analysis, low sample and reagent consumption and high reproducibility due to standardization and automation. Results are delivered within 30-40 minutes in high quality digital data and can be shown in gel-like image, electropherogram and tabular formats.
Features of DNA chips (DNA 1000, DNA 7500, & DNA 12000 kits): Minimal sample consumption - only 1 µL of sample required per analysis; 12 samples can be analyzed in each chip. Sizing accuracy - normalization to two internal markers and ladders. Quantification accuracy and reproducibility - automated quantification of each DNA fragment against internal standards. High resolution of a large number of bands - critical for any multiplex PCR application. Broad linear dynamic range - enables the detection of less abundant products, e.g. low abundance messages in multiplex RT-PCR amplifications or non-specific amplifications. Sensitivity - Laser Induced Fluorescence (LIF) detection for fragments down to 0.1 ng. Ready-to-use - standardized assays and pre-packaged reagent kits.
Features of RNA chips (Small RNA; RNA 6000 Pico and Nano kits): Minimal sample consumption - only 1 µL of sample required per analysis or as little as 5 ng of total RNA or 50 pg of purified miRNA. Fast results - analyze 11 samples in 30 minutes. RNA Integrity Number (RIN) -a reliable tool to compare integrity of RNA samples automatically plus freely accessible. RNA Integrity Database (RINdb) of RNA profiles. Qualitative size analysis of ss- and ds-oligonucleotides - specified within a range of 6 -150 nt, based on an RNA ladder. Ready-to-use - standardized assays and pre-packaged reagent kits.

Applied Biosystems 3130xl Genetic Analyzer: This instrument is a fluorescence-based genetic analysis system. It is fully automated from polymer loading and replacement, to DNA separation, detection, and data analysis enabling 24-hour unattended operation.

Specifications: Autoloading of samples performed from two microtiter plates; either 96- or 384-well format Arrays with sixteen capillaries in four different lengths: 22, 36, 50, and 80 cm. Automated delivery system for POP-4TM, POP-6TM, or POP-7TM polymers Argon laser with primary excitations at 488 and 515 nm Detection of up to 5 dyes for sequencing and fragment analysis CCD detection technology and spectrograph for color separation Simultaneous dual-side illumination detection system to maximize signal uniformity and sensitivity Software for DNA sequencing/base calling (Sequencing Analysis v5.2) and for fragment analysis of microsatellites, SNP, AFLP and LOH (GeneMapper® v4.0) as well as comparative sequencing, mutation detection, and detection of heterozygote insertions and deletions (SeqScape® v2.5)

Beckman Coulter Allegra 25R refrigerated centrifuge; perfect for pelleting DNA from bacteria and yeast, through isolation and purification to post-reaction cleanup.
Specifications: Operating temperature: -2º C to 40º C. S5700 swinging-bucket rotor for 2 microplates TA-14-50 rotor for 8 x 50 ml tubes TA-15-1.5 rotor for 30 x 1.5 ml microtubes

Thermo Savant DNA110 SpeedVac centrifuge is a dedicated centrifugal concentration system for drying low-volume ethanol or isopropanol precipitates of DNA and RNA. The integrated system combines the concentrator and chemically resistant vacuum pump (oil-free ETFE diaphragm).
Specifications: Pump displacement: 36 liters/min (@60Hz), 30 liters/min (@50Hz) Ultimate vacuum level: 7 torr (9 mbar) Rotors for 2 microplates and 24 x 1.5 ml microtubes Chamber heater operating temperatures: Low (ambient), Medium (43°C), or High (65°C).

Eppendorf Mastercycler ep Gradient S thermal cycler in 96-well format. Peltier elements control the temperature of the silver coated block with extremely fast heating and cooling rates.
Specifications: Intuitive graphic programming Heated lid with integrated ESP technology (Electronic Sample Protection) Highest temperature speed due to silver block: up to 6°C/s Gradient block with SteadySlopeTM technology allows freely programmable temperature gradient over 12 rows. Availability of a gradient range from 1° to 24°C enables easy optimization of PCR components.

Eppendorf epMotion 5075 VAC automated pipetting workstation enables fast and reproducible liquid handling for a variety of applications. The 5075 VAC system can pipette from single tubes, plates or reservoirs to 24-, 96- and 384-well plate formats as well as handling specified labware with a gripper tool. Applications include dispensing from a supply (eg, from a supply tub to a 384-well plate), transferring samples from individual tubes, dilution and mixing of samples and automation of the dispensing steps of diverse methods such as nucleic acid purification, PCR setup, cleanup of sequencing reactions, etc. An integrated vacuum station can also be used for high throughput nucleic acid isolation and purification.

Specifications: Workstation has 12 rack positions in 96/384-well standard plate formats Maintenance-free piston-stroke dispensing system Precise, reproducible dispensing from 1 µl to 1,000 µl Automatic exchange of all tools (three volume ranges, single- or 8-channel) Labware handling with gripper tool Optical Sensor for high-precision and contact-free liquid level sensing as well as recognition of tips and labware epMotion Editor software package for generating and editing methods as well as printing and archiving program processes; the drag-and-drop interface is extremely easy to use and intuitive Labware database with more than 300 validated entries can be used to individually compile the system configuration in relation to plates, tubes and liquid classes.

MJ Research PTC-100 thermal cycler uses Peltier technology to electronically deliver accurate heating and cooling over the full temperature range of 0°-100°C

Specifications: Hot Bonnet® heated lid incorporates a thumbwheel to adjust height and pressure; this feature ensures tight sealing of reaction vessels-even microplates-during oil-free thermal cycling. Ramping rates of 1.4°/sec for 0.2 ml tubes or V-well plates. Temperature homogeneity: ±0.5°C within 30 sec of arrival at 60°C. Memory stores approximately 320 programs, and cycler comes with 8 preprogrammed protocols-any sequence of temperatures can be cycled up to 10,000 times. Extremely accurate incubations, with NIST-traceable calibration; any temperature-including below-ambient temperatures-may be held indefinitely, allowing refrigeration after an unattended run. Capacity: 96 x 0.2 ml tubes or 1 microplate.

NanoDrop 8000. The NanoDropTM 8000 spectrophotometer takes full-spectrum UV-Vis absorbance measurements of up to eight samples simultaneously. Using an eight-channel pipette to dispense samples on a linear array of pedestals, the Nanodrop can easily measure 96 samples in less than six minutes.
Specifications: Sample Size: 1 µl Sample Number: up to 8 Path Lengths: 1 mm and 0.2 mm Light Source: Xenon flash lamp Detector: 2048-element linear silicon CCD Wavelength Range: 220-750 nm Detection Limit: 2 ng/µl (dsDNA) Maximum Concentration: 3700 ng/µl (dsDNA)
Applications: Nucleic Acids - concentration and purity of DNA & RNA Protein A280 - concentration and purity of protein Micro Array - dye incorporation concentration and purity of nucleic acid Proteins & Labels - concentration dye-labeled proteins, conjugates, and metalloproteins. BCA, Bradford, Lowry, Pierce 660 - assays for protein concentration UV/Vis - general UV-Vis measurements Cell Cultures - absorbance (light scattering) measurement of suspended microbial cells

OmniLog Phenotype Microarray System. Biolog, Inc. has developed a proprietary technology called Phenotype MicroArrays (PMs). PMs are sets of 96-well microtiter plates with each well containing a different cell culture medium that is designed to test a unique phenotype or cell function. After inoculation with a cell suspension, the plates are placed in the OmniLog incubator-reader, typically for 24 to 48 hours, and the phenotypic behavior is recorded by a CCD camera. The response of the cells in each well is monitored colorimetrically using a patented redox chemistry that integrates the respiration of the cells over time. The result is a color change, from colorless to purple. If the cells display an expected phenotype and can grow in a well, they respire normally to give a dark purple color. If the phenotype and growth are weak, they respire more slowly and give a light purple color. If the phenotype and growth are negative, the well remains colorless. The current PM technology is developed for use with diverse microbial cells including fungi as well as bacteria.

Specifications: OmniLog incubator capacity is 50 standard microplates or PM plates (aka: panels) Incubation Temperature Range: 22° to 45°C in the tray chamber at full capacity Phenotype MicroArray (PM) panels of up to 1,920 phenotypic tests for Gram-negative and Gram-positive bacteria, yeast and filamentous fungi, and mammalian cells OmniLog PM software contains a suite of algorithms that work in conjunction with the OmniLog reader and Biolog's PM panels. These programs allow display of kinetic PM panel data recorded by the OmniLog reader, manage and analyze the data, export it in a variety of raw and processed forms. The OmniLog® PM System generates a kinetic response curve for all assays simultaneously and monitors most known aspects of cell function. The range of phenotypes analyzed includes: Nutrient uptake and transport functions Catabolism of carbon, nitrogen, phosphorus, and sulfur Biosynthesis of small molecules Biosynthesis of polymeric macromolecules Formation of cellular structures Cellular respiratory functions

ROCHE LightCycler® 480 real-time qPCR system. The LightCycler® 480 system is a multiwell-plate based real-time PCR platform which is used for highly accurate qualitative and quantitative detection of nucleic acids and genotyping. Innovative technological enhancements in the LightCycler® 480 instrument provide rapid and accurate real-time PCR data generation and analysis. The sophisticated design of the silver thermal block cycler unit, optical system, and software function to deliver high sensitivity, accuracy, and reproducibility across the entire multiwell plate, independent of sample position. The pre-installed software package includes automated analysis modules for melting curve or endpoint-based genotyping as well as absolute and relative quantification.

Specifications: Reaction volumes: 5 µl - 20 µl (384-well), 10 µl - 100 µl (96-well) Temperature control: Peltier-based heating/cooling from 37° C - 95° C Heating rate: 96-well block: 4.4° C/s; 384-well block: 4.8° C/s Cooling rate: 96-well block: 2.2° C/s; 384-well block: 2.5° C/s Excitation source: Xenon Lamp (430-630 nm) Detector: Cooled monochrome CCD camera (1024 x 1344 pixels) Filters: Excitation: 440, 465, 498, 533, & 618 nm Detection: 488, 510, 580, 610, 640, & 660 nm Preinstalled software: Absolute Quantification; Tm Calling; Absolute Quantification Analysis; Relative Quantification Analysis Endpoint Genotyping; Melting Curve Genotyping

Stratagene Mx3005P Real-Time PCR System. Real-time or quantitative PCR (QPCR) allows researchers to quickly and easily quantify nucleic acids for studying gene expression, mutational analysis, disease state, and gene dosage. QPCR measures PCR product accumulation during the exponential phase of the reaction and before amplification becomes vulnerable to limiting reagents and cycling variability. Fluorescent QPCR data provides accurate information on initial starting copy number. Using QPCR, amplification and detection are combined in a single step and in a single closed tube. This eliminates the need for numerous post-PCR manual steps, and reduces the possibility of introducing variability or laboratory contamination. The Mx3005P system has an open format that allows closed-tube real-time PCR detection with many chemistries including SYBR Green dye and fluorogenic probe systems, detecting up to five different dyes simultaneously. The Mx3005P system supports both real-time and plate read experiments.

Specifications: Excitation source: Quartz-tungsten halogen lamp Excitation range: 350 to 750 nm Detector: Photomultiplier tube (PMT) Detection range: 350 to 830 nm Filters: FAMTM/SYBR® Green I (492nm-516nm), HEXTM/JOETM/VICTM (535nm-555nm), ROXTM/Texas Red® (585nm-610nm), Cy5TM (635nm-665nm) and Cy3 (545-568) Thermal system: Peltier-based, 96-well block thermal cycling system; temperature range 25-99°C Sample format: Standard 96-well plates, 8-strip tubes, 200 µl tubes, optimized for 25µl reactions Linear dynamic range: 10 orders of magnitude, standard curve method Temperature uniformity: +/- 0.25 °C at 72 °C; ramp rate: up to 2.5 °C/second Amplification rate: standard 40 cycle 2-step QPCR reaction completed in 90 minutes. Discrimination: distinguish samples with 5,000 and 10,000 template copies with a 99.7% confidence level

VIBRATOME UltraPro 5000 Cryostat. The UltraPro 5000 open top cryostat has a comprehensive specification and offers the ultimate in precision and constant reproducibility in the preparation of frozen sections. Backed by years of cryostat technology, the UltraPro 5000 cryostat has the 5040 rotary retracting microtome installed and is capable of sectioning a diverse range of hard and soft tissues, plastics, rubber, bone, man-made fibers, wood and many other materials.

Specifications: Minimum chamber temperature: -35°C Specimen temperature control; Fast reacting from +5°C to minimum chamber temperature Quick Release Feather Blade Holder Specimen quick freezer running at -80°C Section range: 0.5 to 30 µm

Qiagen QIAcube uses advanced technology to process Qiagen spin columns, enabling seamless integration of automated, low-throughput sample prep into the laboratory workflow. All processing steps are performed by the QIAcube - from sample lysis to elution of highly purified nucleic acids or proteins. The QIAcube is preinstalled with protocols for purification of plasmid DNA, genomic DNA, RNA, viral nucleic acids, and proteins.

Specifications: Capacity: up to 12 samples per run Pipetting range: 5-900 µl Shaker: 100-2,000 rpm; heating range, ambient temperature to 70° C Centrifuge: 12,000 x g maximum; 12 rotor positions Reagent bottle rack: holds up to six 30 ml bottles Optical & Ultrasonic sensors: check samples, consumables and liquid loading for each protocol run

QIAGEN BioRobot 8000 Gene Expression. The BioRobot 8000 series of molecular biology workstations is designed for high-throughput, walk-away nucleic acid purification using QIAGEN chemistries. An 8-channel pipetting system rapidly performs routine liquid-handling tasks with precision for the 96-well plate format. The robotic handling, automated vacuum, reagent and buffer delivery systems ensure high-performance processing without operator interaction.

Specifications: QIAsoft Operating System v 4.0 controls operation of all components through protocols for DNA and RNA purification. The BioRobot 8000 components: worktable, technical tower, robotic arm, robotic handling system, dilutor system, high-speed dispensing system, wash station, automated vacuum system, cooling and heating system, and high speed shaker system. QIAsoft Gene Expression protocols: RNeasy 96 Universal Tissue Protocol and QIAprep 96 Turbo Microtiter/Elution Microtube Plate Protocol.

QIAGEN TissueLyser provides rapid and efficient disruption of cells and tissues for the BioRobot. Processing of up to 2 x 96 samples takes as little as 2 - 4 minutes. Disruption is achieved through the beating and grinding effect of beads on the sample material as they are shaken with the sample in a variety of grinding vessels. The optimized design of TissueLyser Adapter Sets ensures that tubes remain securely sealed during disruption. This prevents cross-contamination, which is especially important for highly sensitive downstream applications, such as real-time RT-PCR or microarray analysis.

ZEISS Axioplan 2 Imaging System incorporates a research quality light microscope equipped for brightfield, phase contrast, Nomarski differential-interference contrast, and epifluorescence observation with UV, FITC, Acridine Orange and Rhodamine filter sets. Image acquisition is achieved with the ZEISS AxioCam color digital camera with image resolution up to 3900 x 3090 pixels. Image acquisition, processing and analysis are achieved using ZEISS AxioVision v4.5 software. For more details, see Services > Imaging menu.

ZEISS LSM 5 PASCAL laser scanning module is attached to the Zeiss Axioplan 2 light microscope. This enhanced imaging capability provides true confocal or laser scanning technology for the examination of cells and tissues that are labeled with one or more fluorescent probes. Confocal imaging permits greater resolution of thick specimens and localization of organelles and gene expression labeled by very specific fluorescent probes. The Pascal is equipped with Ar (458, 488, & 514 nm excitation) and He/Ne (543 nm excitation) lasers.

LSM 5 PASCAL scan module utilizes two independent galvo scanning mirrors to obtain large scan fields and high resolution images up to 2,048 x 2,048 pixels. This module also has two confocal channels and one transmitted light channel, all with highly sensitive photomultiplier detectors. All moving components of the scan module, such as emission filter wheels, main and secondary dichroic beam splitters, the pinhole and mechanical attenuators for each laser line, are computer controlled. Other features include flexible scan strategies for 3D and time series imaging, continuously adjustable pinhole for optimum Z resolution, precisely controllable laser intensities to protect specimens, and multifluorescence imaging without cross talk between channels.