Equipment in the Biomolecular Research Facility

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Equipment in the Biomolecular Research Facility

Statements of resources for grant applications

DNA Sciences

Mass spectrometry

Shared Instrumentation

Instruments in DNA Sciences

Illumina Genome Analyzer II


  • whole chromosomes
  • targeted studies of genomic regions
  • whole genomes
  • BACs


picture of Illumina genome sequencer

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

picture of ABI 3730 DNA sequencer

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

rpicture of real time PCR machine

Affymetrix Gene Chip System for studying changes in gene expression

fluidics station for washing chips

picture of Affymetrix fluidics station
hybridization oven used for hybridization of cDNA to gene chip geneovencropped.JPG

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

picture of Agilent Bioanalyzer

NanoVue spectrophotometer

for absorbance readings of small volumes, often used to quantitate DNA

Nanovue spectrophotometer small

Bio-Rad QX200™ Droplet Digital™ PCR System

The droplet generator divides the sample, with primers and PCR mix into 8 batches of 20,000 nanoliter sized droplets using water-oil emulsion technology. The DNA is amplified in the thermo cycler, then the reader measures fluorescence in each droplet single file fashion. readeIncludes droplet generator, droplet reader, plate sealer, thermo cycler


ddPCR reader

ddPCR droplet former

Molecular Devices Gemini fluorescent plate reader

can quantitate DNA with PicoGreen and RNA with RiboGreen
More information in Shared Instrumentation section

fluorescent plate reader for 96 well plates in Shared Instrumentation Facility

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.

picture of Orbitrap mass spectrometer

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.

picture of Thermo Electron TSQ mass spectrometer

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.

picture of Bruker MALDI mass spectrometer
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.
fluorescent plate reader for 96 well plates in Shared Instrumentation Facility

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
Dionex HPLC

AVIV 410 Circular dichroism spectropolarimeter

For studies on tertiary structure of proteins.
Operated by researcher. Fee for use.
Brief background on operation here.

picture of circular dichroism spectropolarimeter

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.

Aperio ScanScope slide scanner for converting micrsocopy slides to digital images

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.

GS-800 scanner

fortéBIO Octet RED96 uses BioLayer Interferometry with disposable probes to measure association and dissociation rates of pairs of molecules and hence dissociation constants.
This instrument can perform 8 simultaneous readings. It can also perform quantitation measurements including some equivalent to ELISA,

forteBIO Octet

Acea RTCA cell analysis instrument

real time, continuous measurement of cellular activity, including migration, based on impedance measurements

RTCA instrument

Biotek ELx800 absorbance plate reader

absorbance measurements on microtiter plates at 450, 562, 600, 660 nm

Absorbance plate reader

Electrophoresis related equipment

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



IEF apparatus