Bioinformatic Resources


Computers for Next Generation sequence analysis:

Dell Studio XPS 9000 Dell 7600
24 GB RAM 250 GB RAM
3 TB disk space 4 TB disk space
CLC Genomics NGen/DNaStar

Software's available :

The above computers gives us the flexibility of assembling data
   (de novo and template) from different Next Generation sequencing platforms:

Additional Software's available:

Genomics


Nanodrop ND-1000

User Guide

Qubit 2.0 Fluorometer

How does Qubit work? Who should use Qubit?

User Guide

Cellomics

Cellometer Vision


An automated cell counter and analyzer that combines brightfield and multi-channel fluorescence to generate cell count & florescence data.

User Guide

Transcriptomics

Maui Hybridization System

Our 4 bay system provides containment and active mixing action and constant incubation temperature. The mixers allow for a reduction of hybridization volume (down to 38 µl). Hybridization of slides from various vendors ( Aigilent, Exiqon, Invitrogen, NimbleGen, Operon, and Phalanx Biotech) can be performed in this instrument.

  • Applied Microarrays
  • Agilent Technologis
  • Exiqon microarray
  • Invitrogen
  • NimbleGen
  • Operon
  • Phalanx Biotech

User Guide

Axon GenePix 4000 Scanner

  • This scanner allows DNA, protein, tissue, and cell microarray scanning
  • 5umm pixel size
  • Dynamic monitoring of laser power
  • User selectable laser power
  • One touch calibration and scanner matching

User Guide
GenePix software

ABI 7900HT Fast Real-Time PCR System

This is Real-time PCR instrument used for Quantitative study of gene expression, genotyping, SNP analysis, pathogen detection and measuring RNA interference. The instrument is located in Room 308.

  • Fast PCR option reduces run time to about 35 minutes in a standard 96-well format, or about 55 minutes in a 384-well plate.
  • Continuous wavelength detection from 500-660 nm allows the use of multiple fluorophores in a single reaction.
  • Measure gene expression levels, detect and quantitate pathogens, perform allelic discrimination (SNP genotyping) assays as well as score the presence of gene sequences.
  • 96- or 384-well plate compatibility -- including the TaqMan® Low Density Array.
  • Optional Enterprise edition software provides data analysis tools that support 21 CFR Part 11 guidelines providing data integrity and security.
  • Proven assay development guidelines save time and money

User Guide/Getting started guide

Proteomics

Luminex 200

This is a multiplexing immunoassay system

  • Beads labeled with varying ratios of two fluorescent dyes, and can resolve 100 different dye sets
  • Classify and quantify up to 100 analytes / well in a micotiter plate.
  • Analyze from one SNP in one individual up to 50 SNPs in unlimited numbers of individuals
  • Liquid reaction kinetics enables faster and more reproducible results
  • It's open architecture platform allows leading companies to provide compatible kits and software.
  • The Milliplex Analyst software makes data analysis very easy.

This system allows multiplexing of up to 100 analytes in a single well of a microtiter plate. It's open architecture platform allows leading companies to provide compatible kits and software. The Milliplex Analyst software makes data analysis very easy.

User Guide

2D Gel Electrophoresis

(How to video)

1st dimension:
Protein Isoelectric Focussing (IEF) is a convenient system for separating proteins based on isoelectric point(pI). This used for running IPG strips or iso-electric focusing (IEF) polyachrylamide gel electrophoresis (PAGE). The cell can be used to run multiple IEF strips, with temperature control (10-25°C)

2nd dimension:
First dimension strips are loaded on the second dimension SDS-PAGE gels in a Protean plus Dodeca cell system. This system accommodates up to 12 large gels for high throughput 2D application.

Links to protocols:

GE Typhoon Trio imager

Variable mode imager for RNA, DNA and proteins.

  • Direct blue-excited fluorescence (457, 488 nm)
  • Direct green-excited fluorescence (532 nm)
  • Direct red-excited fluorescence (633 nm)
  • Chemiluminescence

Key features:

  • Single- and multicolor fluorescence via direct laser excitation\
  • Fluorescence imaging (high sensitivity and high resolution
  • Excitation: 20mW 532 nm, 14 mW 488 nm, 10 mW 635
  • Fluorescence imaging (high sensitivity and high resolution)
  • Radio isotopic imaging - quantitate 32P, 33P, 35S, 14C and 3H
  • Excitation: 20mW 532 nm, 14 mW 488 nm, 10 mW 635
  • Emission filters: 390 nm BP, 526 nm SP, 530 nm BP, 555 nm LP, 640 nm BP

User Guide

Ettan Spot Picker

Robotic system

  • Generates protein pick list
  • Accurately pick protein spots from stained or destained gels
  • Transfer the proteins into microplate wells for further analysis
  • Seamless integration with DeCyde™ 2-D Differential Analysis Software

User Guide

Biotek Synergy HT Microplate Reader

The Synergy HT Microplate Reader in room 323 is for fluorescence, absorbance and luminescence measurements and was designed with an emphasis on superior performance in all detection methods.

  • Automatic top and bottom epifluorescence read modes optimized for both sensitive homogeneous and cell-based assays
  • Compatible with Take3 Multi-Volume Plate: sixteen 2 µL microspots for low volume DNA/RNA 260 nm measurements. Saves precious samples, very fast and simple process.
  • Software-controlled automatic probe height adjustment with built-in plate sensor to prevent probe crashes
  • Scanning monochromator for wavelength scans to identify peak absorbance and provide full spectral analysis
  • Luminescence measurements with top detection for best sensitivity
  • Reads 6- to 384-well microplate formats including PCR trays and Terasaki plates
  • Well area scanning for popular cell-based assays
  • Time-Resolved Fluorescence capability
  • Dual Reagent Dispensers
  • USB and serial ports for easy connectivity

Includes Gen5™ Software
KC4

Metabolics

High Performance Liquid Chromatography

♦   Auto-Sampler: SIL-20A/20AC

  • High sped injection and multi-sample processing
  • Prevents carryover and is equipped with a sample cooler.

♦   Detectors

Photo Diode Array -- Sensitive UV-Vis detector, allows Fraction Collector

  • variable wavelength detection across the whole range.

Refractive Index

  • Unique 4 partition PDA technology over a wide concentration range.
  • Analytical
  • Semi-prep
  • Preparative

♦   Fraction Collector

Imaging

Quantity One software

Molecular Imager FX

The phosphoimager at Room 323 is capable of imaging and analyzing a broad range of isotopes including 32P, 33P, 35S, 14C, 3H and 125I.

GE Typhoon Trio imager

Variable mode imager for RNA, DNA and proteins.

  • Direct blue-excited fluorescence (457, 488 nm)
  • Direct green-excited fluorescence (532 nm)
  • Direct red-excited fluorescence (633 nm)
  • Chemiluminescence

Key features:

  • Single- and multicolor fluorescence via direct laser excitation\
  • Fluorescence imaging (high sensitivity and high resolution
  • Excitation: 20mW 532 nm, 14 mW 488 nm, 10 mW 635
  • Fluorescence imaging (high sensitivity and high resolution)
  • Radio isotopic imaging - quantitate 32P, 33P, 35S, 14C and 3H
  • Excitation: 20mW 532 nm, 14 mW 488 nm, 10 mW 635
  • Emission filters: 390 nm BP, 526 nm SP, 530 nm BP, 555 nm LP, 640 nm BP

User Guide

Axon GenePix 4000 Scanner

This scanner allows DNA, protein, tissue, and cell microarray scanning

  • 5umm pixel size
  • Dynamic monitoring of laser power
  • User selectable laser power
  • One touch calibration and scanner matching

User Guide
GenePix software

Additional Core Resources

Milli-Q Advantage A10 Water Purification System

Water Specifications

  • Resistivity 18.2 MΩcm at 25°ree;C
  • TOC ≤ 5 ppb
  • Particulates* (> 0.22 µm/ml) < 1 particulate/ml
  • Bacteria* < 1 cfu/ml
  • Pyrogens (endotoxins)* < 0.001 EU/ml
  • RNases* < 0.01 ng/ml
  • DNases* < 4 pg/µl
  • Flow Rate up to 2 l/min

*Test conditions with the appropriate Q-POD final polisher. These values are typical and may vary depending on the nature and concentration of contaminants in the feed water.

Beckman Biomek 2000 Station

The Biomek 2000 located in Room 308 is a high-throughput liquid handling robot.

♦   Applications in Immunology

  • ELISA
  • EIA
  • RIA

♦   Applications in Molecular Biology

  • DNA Sequencing
  • DNA Fingerprinting
  • PCR Processes
  • DNA Template Preparation

User Guide