Bioinformatic Resources
Computers for Next Generation sequence analysis:
| Dell Precision 7920 Tower |
Dell 7600 |
| 128 GB RAM |
250 GB RAM |
| 2 TB x 7 disk space |
4 TB disk space |
| CLC Genomics |
Sequencher |
Software's available :
The above computers gives us the flexibility of assembling data
(de novo and template) from different Next Generation sequencing platforms:
- Ion Torrent
- Illumina
- Helicos
- PacBio
- Sanger method
Additional Software's available:
- full-spectrum UV-Vis absorbance analyses (220-750nm)
- for measuring absorbance of DNA, RNA, dyes, proteins and microbial cell culture OD
- One µl of sample
- Large dynamic range: 2-3700 ng/µl of dsDNA
- No dilutions for most samples
- Cuvette position available
- Ten second measurement
User Guide
- full-spectrum UV-Vis absorbance analyses (220-750nm)
- for measuring absorbance of DNA, RNA and proteins OD and quantitative assays.
- Large LCD color touch screen
- Easy workflow navigation to save time
- Automatic data logging and USB port
- Standard curve display after calibration is complete
How does Qubit work?
Who should use Qubit?
User Guide
An automated cell counter and analyzer that combines brightfield and multi-channel fluorescence to generate cell count & florescence data.
User Guide
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
- 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
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
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
(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:
User Guide
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
The Synergy H1 Microplate Reader in room 332 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
Includes Gen5™ Software
KC4
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
Quantity One software
The phosphoimager at Room 323 is capable of imaging and analyzing a broad range of isotopes including 32P, 33P, 35S, 14C, 3H and 125I.
User Guide
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
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.
The Biomek 2000 located in Room 308 is a high-throughput liquid handling robot.
♦ Applications in Immunology
♦ Applications in Molecular Biology
- DNA Sequencing
- DNA Fingerprinting
- PCR Processes
- DNA Template Preparation
User Guide