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Equiment in the Biomolecular Research Facility

Biomolecular Research Facility

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Equiment in the Biomolecular Research Facility

Statements of resources for grant applications

Mass spectrometry

Shared Instrumentation

Instruments in DNA Sciences

Illumina Genome Analyzer II for: whole chromosomes targeted studies of genomic regions whole genomes BACs
Illumina MiSeq sequencing system capillary electrophoresis sequencing multiplexed PCR amplicon sequencing small genome sequencing small RNA sequencing library quality control 16S metagenomics See newsletter for more information
ABI 3730 DNA Analyzer DNA sequencing
ABI Prism® 7900HT Sequence Detection System for real time PCR measurements quantitation of gene expression mutation detection allelic discrimination single nucleotide polymorphisms (SNP) characterization and screening microRNA quantitation DNA copy number determination viral titration
Affymetrix Gene Chip System for studying changes in gene expression fluidics station for washing chips
hybridization oven used for hybridization of cDNA to gene chip
laser GeneArray scanner for measuring amounts of bound probes
Agilent BioAnalyzer This microfluidics based instrument uses electrophoresis for rapid quality control on small samples of DNA and RNA. Minimum concentration is about 0.1 ng/µL, and 1.5 µL is loaded. Separation is by size, similar to a conventional gel
Nanovue spectrophotometer for absorbance readings of small volumes, often used to quantitate DNA
Molecular Devices Gemini fluorescent plate reader can quantitate DNA with PicoGreen More information in Shared Instrumentation section

Equipment in the Mass Spectrometry Core

Thermo Electron LTQ Velos Orbitrap Mass Spectrometer The first part of this instrument has two linear ion traps for more efficient operation. Species of interest can be analyzed with high accuracy in the Orbitrap section. equipped with Collision Induced Dissociation (CID), Electron Transfer Dissociation (ETD), Higher-Energy Collision Dissociation (HCD) and a microspray ion source for complex mixture and PTM analysis as well as relative quantification.
Thermo Electron TSQ Quantum Access MAX Equipped with Quantitation-Enhanced Data-Dependent MS/MS (QED-MS/MS) and Highly Selective Reaction Monitoring (H-SRM) to provide accurate quantification at low levels for specific molecules of interest. Adapting this instrument to perform Selective Reaction Monitoring (SRM)/Multiple Reaction Monitoring on small samples started in December 2009 This triple quadrupole instrument is used for quantitation of proteins, peptides, some metabolites.
Bruker MicroFlex MALDI This instrument measures masses of intact molecules. Sample preparation is usually relatively simple so this instrument is the first choice to obtain the mass of peptides, proteins and some other molecules.

Thermo and Agilent HPLC systems coupled to above mass spectrometers

Equipment in Shared Instrumentation Core

The Biomolecular Research Facility has equipment which is either not commonly found in individual laboratories or is needed only occasionally by some laboratories. Some equipment is operated by facility personnel, and some is used by individual researchers. Contact John Shannon ph. 3-9399 about use of the equipment listed below.

Molecular Dynamics Gemini EM Spectramax Fluorescent plate reader For fluorescence readings of plates with 384, 96, 24, 12, 6 well microtiter plates. Dual monochromator optics. Does not perform absorbance readings. Operated by researcher. Fee for use.
High performance liquid chromatography. ABI 140 for 1 and 2 mm diameter columns Beckman System Gold for 4.6 mm diameter columns. Dionex Ultimate for 0.3 to 4.6 mm diameter columns. All above systems have a variable wavelength UV detector. Used for separation of peptides, proteins and some other molecules, usually with reverse phase columns. Medium pressure chromatography using FPLC Amersham AKTA FPLC, detection at 280 nm (or 260 nm), with a Frac-100 fraction collector. gel filtration, ion exchange, for separation of proteins and peptides
AVIV 410 Circular dichroism spectropolarimeter For studies on tertiary structure of proteins. Operated by researcher. Fee for use. Brief background on operation here.
Aperio Scanscope Slide Scanner Aperio ScanScope to scan microscope slides at 20X, 40X, 63X (resolutions of 0.5, 0.25, 0.17 micron/pixel) for digital pathology. The scans can be exported as TIFF or JPEG files. The scanner can scan a batch of 5 slides.
Gel and film scanners Bio-Rad GS800 for absorbance readings on gels or blots at visible wavelengths and X-ray film. Three wavelength filters for different stains. ImageQuant software for image analysis available Bio-Rad FX fluorescent scanner. Three lasers and five filters to cover common fluorescent stains. Multiple stains can be scanned and overlaid. Both scanners produce files which can be converted to 8 or 16 bit tiff files.
Biacore 3000 for biomolecule interactions Used to determine kinetics of binding between biological molecules
Roche RTCA cell analysis instrument real time, continuous measurement of cellular activity, including migration, based on impedance measurements
Biotek ELx800 absorbance plate reader absorbance measurements on microtiter plates at 450, 562, 600, 660 nm
Electrophoresis related equipment Bio-Rad Proteome Works Spot Cutter allows automated cutting of gel plugs and cutting of gel plugs from gels stained with Sypro Ruby dye or visible dyes. Isoelectric Focusing apparatus Amersham apparatus for 18 cm strips Bio-Rad Protean IEF cell for 11, 17, 25 cm strips Bio-Rad Rotofor user operated