Client PC Workstation
Advance Reservations, made through the Biosci-Booked (Genomics), are required for use of this computational resource (Computer-Workstation.jpg) in the Genomics Facility. The computer has a variety of genomics-related software (see List) with associated User Guides, as well as standard Microsoft Office software. For descriptions of some of the ABI software, please see Data Analysis on the 'Services' page for the ABI 3130xl platform. Suggestions for additional 'genomics' software are welcome.
The Client PC Workstation is accessible strictly through LSU's network; contact the facility to obtain the computer name required to make a Remote Desktop connection. Clients must adhere strictly to the schedule in Biosci-Booked (Genomics); otherwise, analyses might be lost when they log in while someone else is already using the computer. When accessing this resource from off-campus, your computer must have the LSU-approved VPN installed and connected. Finally, clients must log on to the computer with their LSU credentials; however, such logins do not count against their allotment of "5 LSU PC registrations".
Applied Biosystems (ABI) software
- Protein Thermal Shift (PTS), v1.4
- GeneMapper, v5
- PeakScanner, v2
- Primer Express, v3.0.1
- QuantStudio qPCR, v1.3
- Sequence Analysis, v6
- Sequence Scanner, v2
- SeqScape, v3
- Variant Reporter, v2
- Bioanalyzer, vB.02.10
- Editseq, v5
- Megalign, v5
- PrimerSelect, v5
- Protean, v5
- SeqMan, v5
DNASTAR Lasergene software (2001)
ABI ViiA·7 and QuantStudio·6 (qPCR)
These instruments are complete, real-time PCR systems that detect and quantitate nucleic acid sequences. A great feature of these two platforms is that, although they have different outside 'shells', they use exactly the same internal components, calibration standards, and software; thus, users can safely swap back-and-forth between the platforms even within the same experiment. In the rare instance in which an assay uses an unusual combination of dyes, the ViiA·7 does offer additional flexibility by virture of its six decoupled excitation and emission filter channels (which allow for additional dye combinations and maximum multiplexing capabilities).
Primers and probes can be automatically designed with Primer Express® software. In addition to the Quick Guides and the complete User Manuals on our website, you can visit the ThermoFisher website to listen to webinars regarding qPCR and our instruments.
The Thermo Savant SPD1010 SpeedVac is a high capacity instrument for efficient processing of large batches of DNA or RNA samples. We have rotors for 1.5 ml microtubes and for 96-well plates. Typical applications include concentrating DNA extractions and removing low concentrations of non-agressive organic solvents (methanol, ethanol, acetonitrile) from samples. Faster drying can be achieved by setting the temperature to 65oC, and the drying chamber’s automatic bleeder valve prevents sample loss when stopping the rotor.
Qubit 4.0 (fluorometer)
The Qubit 4.0 can be used to quantify dsDNA, ssDNA, RNA, and proteins. This instrument can also be used to assess RNA integrity. All Qubit assays require 1-20 ul of sample, resulting in the quantitation ranges shown with each kit. Samples are analyzed using Axygen 0.5-ml tubes (PCR-05-C, thin-wall, clear). For further information, please see Qubit 4.0 on the facility's Facts & Links webpage.
Prior to each use of this 'self-service' instrument, clients must ask the Genomics Facility staff to prepare the system for operation. Staff will also provide instructions for operation of the Bioruptor, guidance on sonication profiles, and empty the system after use.
To retain the integrity of DNA, Diagenode’s Bioruptor® NGS uses a gentle method of sonication and a chilled water bath to generate indirect sonication waves. As a result, the Bioruptor® produces better and more consistent results than are achieved with harsher sonication methods. Up to 12 closed tubes can be sonicated in parallel and the continuous rotation of tubes allows even distribution of the energy for efficient sonication.
Typhoon 8600 Variable Mode Imager
The Typhoon™ 8600 Variable Mode Imager is capable of fluorescence and storage phosphor (chemiluminescence detection can be an option under certain circumstances) detection of gels and blots. The Typhoon can scan storage phosphor screens (mounted or unmounted), gels and blots (≤35 × 43 cm). Images can be manipulated with ImageQuant™ Image Analysis Software; alternatively, users can change the file extension (i.e., *.gel) to "*.tif" and import the image into other software such as Adobe Photoshop.
This ABI thermal cycler performs standard PCR, including temperature gradients, and it is protected from brief power outages by an APC backup power supply. Normally, all other thermocyclers in the Genomics Facility are reserved solely for use by the Facility or members of the Batzer lab; however, you may request permission to use the other thermocyclers if you can plead extenuating circumstances.