Facilities and Equipment by Room
Main Lab: Pre-Amplification Prep
The main lab at GARP houses the freezers, standard lab equipment and reagents needed to perform pre-amplification experiments on Agilent cDNA arrays, Affymetrix GeneChips®, and Next Generation Sequencing. Several thermal cyclers are located in the main lab but any tubes with amplified products synthesized using these thermal cyclers are opened only in one of the post-amplification labs in order to prevent amplified product dispersing into the pre-amplification area. These thermal cyclers include one single head 96-well PTC-100 plate thermal cycler from MJ Research, Agilent’s SureCycler 8800 (a single-head 96-well plate thermal cycler), one duel-head PTC-200 DNA Engine thermal cycler from MJ Research, DNA Engine Tetrad™ Thermal Cycler also made by MJ Research. The Tetrad™ has the ability to run four 96-well plates at a time and the SureCycler 8800 has adjustable temperature ramp speeds.
The main lab also has the Bio-Rad Gel Doc (Bio-Rad) for imaging electrophoretic gels for DNA SAQC, the Agilent 2100 Bioanalyzer for analyzing RNA and DNA quality, the NanodropTM 1000 Spectrophotometer (Nanodrop Technologies) used for measuring concentration and dye-incorporation of samples and the Invitrogen Qubit 2.0 Fluorometer which is a picogreen technology used to quantitate RNA and DNA. We also house our NanoString nCounter® Prep Station 5s and Digital Analyzer 5s in our pre-amplification room as this assay does not incorporate amplification or enzymology into the prep.
Post-Amplification Room: Microarray Prep
GARP has two separate rooms for post amplification work. The Microarray Post Amplification room contains the array hybridization ovens: two Affymetrix Hybridization Oven 640s and one Agilent DNA Microarray Hybridization Oven. The hybridization area also houses the rest of the equipment used for the Affymetrix GeneChip® platform: the GeneChip 3000 Scanner, which is capable of scanning all of the high density arrays from Affymetrix and two fluidics stations for washing and staining the hybridized arraysArray Fabrication.
Additionally, we have designated lab bench space for prep in our ozone-depleted chamber for working with Cy3- and Cy5-labeled samples for Agilent microarrays. Ozone Solutions’ Ozone Interceptor destroys ambient ozone levels within the chamber at a flowrate of 70 SCFM. We have Aeroqual’s Ozone Monitor NT-70 to confirm ozone depletion within the chamber. A second setup of the Ozone Interceptor, chamber and monitor is used in our mixed prep room with the Agilent SureScan scanner. This ensures that microarrays utilizing ozone-sensitive dyes are not exposed to ozone during scanning. Agilent expression prep requires aRNA purification be performed with centrifugation at 4oC. GARP uses Beckman Coulter’s Microfuge 22R Centrifuge to accomplish column purification in 4oC temperature regulation. This cold centrifuge is also located in GARP’s post-amplification microarray prep room.
Also located in the microarray post-amplification prep room is a Perkin Elmer Victor X3 Plate Reader and a SpectraMax 384 Plus Plate Reader. MAUI 4-bay Hybridization Station (BioMicro Systems) for NimbleGen arrays is also located in this room, however, since Nimblegen discontinued microarray manufacturing, this instrument is currently in storage.
Post-Amplification Room: Sequencing Prep
The Post-Amp Sequencing Room houses the bulk of GARP’s sequencing instrumentation. The Illumina HiSeq 2000 sequencer, Illumina cBot, Illumina MiSeq* and Illumina HiSeq 2200* are located in this room. Here GARP also set up a second Agilent 2100 BioAnalyzer for analyzing RNA and DNA quality as well as the Invitrogen Qubit®. Learn more about the BioAnalyzer and how it greatly improves quantitating RNA samples used in array experiments. It also houses the Luminex 200 system. This is a medium-through put system that allows for mutliplexing up to 100 analytes in a single well. Luminex applications vary from gene expression, miRNA expression, and genotyping.
The iCycler iQ Real-Time PCR Detection System (Bio-Rad), which is used exclusively for processing SuperArray plates, and Eppendorf Centrifuge 5810 are housed in the post-amp sequencing lab.
Intermediate Amplification Room: Mixed Prep
The Intermediate Amplification Room, which is designated for mixed prep stages, is home to GARP’s Labnet Vortemp 56 (for use with Panomics and Luminex assay preps), Covaris shearing instrument, Pippen (Sage Scientific), Applied Biosystems ViiA 7 Real-Time PCR (Life Technologies), and the Thermo Scientific Megafuge 40 centrifuge with array plate rotor.
This room also houses the cDNA array scanner for imaging spotted arrays, the Agilent Microarray Scanner with SureScan High Resolution Technology, which sits inside an ozone depletion chamber.