Genomics facility
We are a shared facility, located in laboratory 19AX02, available for use by anyone within the Faculty of Health and Medical Sciences (FHMS) or Faculty of Engineering and Physical Sciences (FEPS).
Overview
We are a shared facility, located in laboratory 19AX02, available for use by anyone within the Faculty of Health and Medical Sciences (FHMS) or Faculty of Engineering and Physical Sciences (FEPS). The facility hosts equipment for the analysis and quantitation of nucleic acids and protein. All equipment is free to use, but researchers are generally required to provide their own consumables. Researchers must undergo a laboratory induction before working in our lab and a Howie-style lab coat must always be worn.
The laboratory is a clean laboratory, which means no live organisms are allowed to be brought into the lab.
Researchers are entirely responsible for the correct and proper storage of all data generated on all of the equipment in the lab. We have to regularly clean/clear data erroneously stored on the associated computers in order to keep the equipment running smoothly. Most of our computers are networked, and we strongly recommend that you back-up all your data.
Due to COVID-19 restrictions, the current occupancy limit for the room is four people. There is a booking sheet stuck to the wall on the left-hand side of the entrance for track and trace purposes, which must be filled out upon entry to the lab.
Equipment
Equipment | Purpose | Training | Booking |
|---|---|---|---|
-80 freezer | Back-up storage facility | None available | None |
Bioanalyser | Measures quality of nucleic acid sample | Available on request | Online |
Blue Pippin | Electrophoretic DNA-fragment size-selection | None available | None |
Covaris ultrasonicator | High frequency ultrasonication | None available | None |
Microarray scanner | Identification of all nucleic acid species | None available | None |
Miniseq sequencer | Identification of all nucleic acid species | Mandatory | Online |
Nanodrop | Measures quantity of nucleic acid sample | Available on request | None |
Phosphoimager | Imaging of phosphor screens | None available | Paper diary |
QS7 qPCR machine | Identification of specific nucleic acid species | Mandatory | Online |
Quantus fluorometer | Measures quantity of nucleic acid sample | Available on request | None |
Ultracentrifuge | Ultra-speed centrifugation | Mandatory | Paper diary |
Vilber imager | Imaging of colorimetric, fluorescent and chemiluminescent membranes/gels | Available on request | Paper diary |
Equipment details
Overview
We have two ultra-low temperature freezers, which must be kept clear at all times as they are for emergency back-up storage only.
Health and safety
SOP-7
Training and booking requirements
No training required. Cannot be used unless in a freezer break-down emergency, or by prior arrangement with the Systems Biology technical team.
Maintenance
Serviced annually in accordance with the FHMS-wide -80 freezer service contract.
Overview
The bioanalyser is a chip-based microfluidic system which primarily analyses the quality of nucleic acids, both DNA or RNA, but is also capable of measuring quantity. For RNA samples, the machine gives each samples an RNA integrity number (RIN) out of a maximum of 10, which indicates the integrity of your RNA. This is the gold standard in the field and is often asked for by sequencing companies/facilities prior to carrying out RNA-sequencing. Researchers are responsible for purchasing their own reagents and chips, and may then borrow the chip priming station, located in the drawer in 19AX02, in order to load their chips. We are fortunate enough to have two bioanalysers in our lab; one dedicated to RNA and the other to DNA. This is intended to keep the RNA machine free of RNase-contamination.
Health and safety
SOP-41
Training and booking requirements
Online booking via microsoft outlook calendar, details will be given out during the mandatory training session.
Maintenance.
The electrodes are cleaned monthly by the Systems Biology technical team, and the diagnostics are run after every clean to ensure correct reassembly. The syringe in the priming station is changed every six months. The machines themselves are on a yearly annual service contract.
Overview
The Blue Pippin is an electrophoresis agarose-gel based fragment size-selection system, which can be used in place of manual gel purification. Applications include; miRNA isolation, DNA sequencing, RNA-Seq, genotyping, ChIP-seq. It can size-select fragments between 100bp and 50kb, depending upon the agarose gel percentage in the pre-cast gel cassette, by applying either a constant, or pulse-field voltage, across the gel.
Health and safety
None in place as not currently in use – must be written if you intend to use it
Training and booking requirements
No mandatory training provided by the technical team. No booking system.
Maintenance
There is no routine maintenance or service contract for the Blue Pippin.
Overview
The Covaris ultrasonicator is able to perform a broad range of pre-analytical sample preparations, on samples between 25mL to 10mL, using Adaptive Focused Acoustics (AFA). Applications include; Tissue disruption and homogenization, Extraction for metabolic and proteomic profiling, DNA fragmentation, RNA extraction, Nanoparticle formation – micronization, Chomatin fragmentation, Cell, spore and organelle lysis, Compound dissolution, Compound formulation, ADME/Tox extractions. Unlike low frequency sonicators, AFA operates at high frequencies (around 500KHz) and is inaudible. Therefore, precautions for low frequency sonicators such as sound proof boxes and ear defenders are not required.
Health and safety
SOP-45
Training and booking requirements
No mandatory training provided by the technical team. No booking system.
Maintenance
There is no routine maintenance or service contract for the Covaris.
Overview
The Microarray scanner is used for reading microarray chips, for identification and relative quantification of DNA/genes within a sample. DNA/cDNA samples from one or more condition are labelled via a Cy3 or CY5 labelled nucleotide base, and hybridised onto a chip containing a DNA library. The colour of each spot is measured by the scanner, and thus the presence of that gene hybridised to that spot can be confirmed or denied in each sample. Microarray technology has been mostly replaced by next generation sequencing over the last few years.
Health and safety
None in place as not currently in use – must be written if you intend to use it.
Training and booking requirements
No mandatory training provided by the technical team. No booking system.
Maintenance
No maintenance contract for this machine.
Overview
The MiniSeq machine is a next generation sequencing platform, which carries out sequencing of a DNA library by parallel synthesis using fluorescently labelled nucleotides. Data is generated as FASTAQ files, which are then analysed using bioinformatic tools. Researchers are required to provide their own consumables, cartridge and flow-cell, and prepare these in their own lab in accordance with their local H&S protocols.
Health and safety
TRA-726, CRA-1013, SOP-TBC
Training and booking requirements
Mandatory training is required to be undertaken with the technical team prior to first use of the machine. Online booking via microsoft outlook calendar, details will be given out during the mandatory training session.
Maintenance
Routine washing of the machine is carried out once every two weeks by the technical team. The machine is under warranty until September 2021.
Overview
The Nanodrop is a single read spectrophotometer used to quantify nucleic acids (RNA or DNA) or protein using absorbance readings at different wavelengths. It also gives an estimation of contamination of the sample with other contaminants commonly used during DNA/RNA extraction protocols such as phenol and protein.
Health and safety
SOP-134
Training and booking requirements
No mandatory training provided by the technical team. No booking system.
Maintenance
This machine is covered by a service contract with Labtech, which includes an annual service visit by a qualified engineer.
Overview
The Typhoon FLA 7000 is a laser scanner designed to perform biomolecular imaging and quantitative measurements of radioisotopic labels, read from an exposed phosphor screen. Users are prohibited from bringing radioactivity into the laboratory; only the phosphor screen may be brought in for scanning.
Health and safety
SOP-51
Training and booking requirements
There is no mandatory training required. Booking is available via a paper diary located at the machine.
Maintenance
There is no routine maintenance or service contract in place for the Typhoon.
Overview
The QuantStudio7 (QS7) is a quantitative polymerase chain reaction (qPCR) machine, capable of running fast 96-well plates, 384-well plates and arrays cards, for the identification and relative quantification of specific nucleic acids using commercially available or researcher-designed primers. The machine runs a repetitive heating cycle, reading fluorescence at a user-defined stage within this heat pattern, to measure incorporation of fluorescence as double stranded DNA is synthesised. Our machine can run either SYBR green assays or Taqman, and is additionally calibrated for the following dyes; SYBR, NED, ROX, TAMRA, VIC, FAM. Our 96-well block is a fast-block, which means it is capable to shifting temperature at a greater speed than a standard block, permitting users to run either fast or standard chemistries on their 96-well plate.
Health and safety
SOP-53, TRA-147
Training and booking requirements
Mandatory training is required before your log-on to the associated laptop is enabled via the IT team. Training takes an hour and is conducted by the Systems Biology technical team. Once completed, your log-on to the associated laptop will be enabled. Booking is via outlook, by creating an event on your calendar and inviting the equipment to your event (this will be covered in your training session).
Maintenance
The machine is under service contract with ThermoFisher, which includes a yearly service visit by a qualified engineer and enhanced technical support. Calibration of the 96-well and 384-well blocks is carried out by the technical team every 6 months.
Overview
The Quantus fluorometer is used to quantitate nucleic acid (RNA or DNA) by measuring incorporation of a fluorescent dye. It uses a standard curve of known concentrations, in order to calculate the concentration in your unknown sample(s). It is a competitor to the well-known Invitrogen Qubit, and works in the same way. Fluorescence-based technology is considered a more accurate method for quantitation than the absorbance-based technology used by spectrophotometers such as the nanodrop. However, sample prep is more complicated and requires additional reagents, so the Quantus is often only used when a truly accurate measurement is required e.g. for sequencing. Users are required to purchase their own reagents, available from Promega.
Health and safety
TRA-292, SOP-169
Training and booking requirements
There is no mandatory training required, and no booking system
Maintenance
There is no routine maintenance or service contract for the Quantus.
Overview
We have two Beckman ultracentrifuges, capable of accepting multiple different fixed angle and swinging bucket rotors. The rotors which we have within the lab, which are available to borrow are; 70.1Ti, 70Ti, SW41Ti and SW55Ti. Please refer to the Beckman website for specifics such as maximum speeds and tube types required for each rotor. Alternatively, users are welcome to bring their own rotors with them. Users are required to provide their own consumables e.g. tubes.
Health and safety
TRA-118, SOP-87
Training and booking requirements
Mandatory training is required to be undertaken with the technical team prior to first use of the ultras. The machines are bookable via a paper diary located next to the machine.
Maintenance
The XPN-80 is our newer ultra, and is still under warranty with Beckman which includes a yearly service visit. The older XL-100 is on the FHMS-wide centrifuge service contract, and this includes an annual service.
Overview
The Vilber Imager is an all-in-one system capable of imaging chemiluminescent, fluorescent and colorimetric samples, gels or blots. A fast cooling camera captures high resolution digital images of labelled protein and nucleic acid bands resolved by electrophoretic or Western blotting separation methods.
Health and safety
TRA-453, SOP-247
Training and booking requirements
No mandatory training provided by the technical team. Booking is via a paper diary located at the machine.
Maintenance
The machine is current under extended warranty, expiring 2022.
Contact us
Please contact the technical team in charge of the facility for further information.
- Email: systemsbiologytechteam@surrey.ac.uk
- Telephone: +44 (0)1483 686498
- Mobile: +44 (0)7866 459744
- Location: 33AX01
Lab team
The laboratory is supported by the Systems Biology technical team.
Dr Helen King
Lab Manager (shared post)
Dr Mandy Fivian-Hughes
Lab Manager (shared post)
James Childs Hunt
Lab Technician