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The USF Genomics Equipment Core is a NextGen Sequencing laboratory facility which consolidates resources and expertise to provide genomics laboratory training from the Library preparation to Next Generation Sequencing. The core offers assistance with experimental design, trouble shooting, and data analysis. Certified users may reserve time in the USF Genomics Equipment Core for library prep and sequencing. Completion of the USF Genomics RNAseq Laboratory Training is required to become a certified user of the Core. The following services are available for USF users:
Equipment for NextGen Sequencing:
- Illumina - NextSeq-500
- Illumina - MiSeq System
- 10X GENOMICS- Single Cell Instrument - Chromium Controller
Instrumentation for library-prep and quality-assurance:
- Agilent - TapeStation 2200, TapeStation 4200 (DNA and RNA quality assessment)
- Invitrogen Qubit 2.0 fluorometer (DNA and RNA sample quantification)
- Roche - LightCycler 96 Real-time PCR Instrument (DNA library quantification)
- Covaris - M220 Focused Sonicator (DNA fragmentation)
The USF Genomics Core now uses iLab for all project-specific communications (quotes, service requests, equipment reservations). In order to use iLab, users must create a free account with their USF email. Specifics on how to create an account and submit a request may be found in the iLab Instructions for PIs and Certified Users.
USF Genomics Equipment Core iLab Homepage: https://my.ilabsolutions.com/service_center/show_external/5175
If you have an inquiry about general pricing, see the 'USF Genomics Core Rate Sheet' below.
Questions regarding the USF Genomics Equipment Core can be sent to [email protected] At this time, core services are only available to USF users.
The scientists are supported by our highly experienced technical staff. A wide range of high-end equipment as well as different aquaria-rooms are available for the different kind of research projects.
cold water aquaria system
Our cold water aquaria system contains 122 aquaria with a total volume of 33’000 L. More than half of the aquaria are connected to a flow-through system which provides the aquaria with a constant supply of fresh water from Lake Lucerne. The remaining aquaria are filtered with an air filter connected to the centralized compressed air system.
Our cold water aquaria vary from small 150 L rearing aquaria, up to a large 2250 L tanks. We also have many small aquaria which can be set up as required.
warm water aquaria system
Our warm-water aquaria system consists of 385 aquaria (41’000 liters in total) distributed among three rooms.
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The main room, containing 345 aquaria with a total volume of 31’000 L, has a central filtration unit with a sedimentation tank, sand-filter, bio-filter and a UV-C unit to maintain optimal water conditions for the fish.
The aquaria in the other rooms are filtered with an air filter connected to the centralized compressed air system.
Our aquaria vary in size from small 20 L breeding tanks, up to six meter experimental aquaria and a large 4700 L round tank for behavioral experiments.
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We have two large outdoor observation tanks with a glass wall along one side to allow observations of fish behavior.
The two observation tanks are 10 x 3 x 1.05 m and 15 x 3 x 1.4 m, with a combined volume of 94’000 L. The tanks can be partitioned lengthwise and crosswise to create smaller compartments.
These tanks are connected to a flow-through system with a continuous supply of fresh water from Lake Lucerne.
Our state-of-the-art facilities provide infrastructure for a wide range of research in molecular population genetics and evolutionary ecology.
We are associated with the ETH Genetic Diversity Center (GDC), where additional applications, such as pyro-sequencing are available. Further, the GDC provides bioinformatics support and computing facilities for our large genomic data sets.
For Next Generation Sequencing (NGS) we work with our sequencing center in Berne and University of Lausanne or outsource our prepared DNA libraries to commercial sequencing centers.
The laboratories are used by our research staff, students as well as by visiting scholars.
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List of applications and available instruments at the CEEB lab:
- Library preparation for Next Generation Sequencing (NGS)
Currently, we prepare RADtaq and whole genome libraries for the Illumina HighSeq sequencing platform
- DNA shearing (Covaris M220)
- DNA size selection (Sage ELF)
- DNA quality control (Agilent TapeStation)
- Automated DNA/RNA extraction
- Homogenizing of tissue samples (Qiagen TissueLyser II System)
- DNA purification with magnetic beads (Qiagen BioSprint 96 Robotic Workstation)
- DNA/RNA amplification and quantification
- Standard and gradient thermocyclers
- ABI real time PCR machine
- Roche LightCycler 480
- Sequencing and fragment analysis
- Fragment analysis (Microsatellites, RFLP) and Sanger sequencing
- ABI 3130XL DNA Analyzer (16-capillary)
- CEQ8000 Beckman Coulter sequencers (8-capillary)
- Data analysis
In our data analysis room we have 4 computers (Mac and PC) equiped with dedicated analysis software packages including CLC Genomics Workbench, GeneMapper, GenMarker, Sequencher, PAUP, MacClade.
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The Genetic Diversity Center (GDC) provides bioinformatics support and computing facilities for our large genomic data sets.