Genomics facility

Overview

We have one ultra-low temperature freezer, which must be kept clear at all times as it is 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 bioanalyzer 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. 

Health and safety

SOP-41

Training and booking requirements

No mandatory training provided by the technical team. Online booking via microsoft outlook calendar, please contact us for details.

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 machine is under service contract with Agilent, which includes a yearly service visit by a qualified engineer and enhanced technical support.

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 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-412

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 service contract with Illumina, which includes a yearly service visit by a qualified engineer and enhanced technical support.

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

CRA-1100, 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

The Qubit fluorometer is used for the accurate quantification of RNA, DNA and protein by detection of a fluorescent dye incorporated into the nucleic acid or protein. 

Like the Quantus fluorometer it uses a standard curve of know concentrations to calculate the concentration of your unknown samples. The two systems are competitors and work in similar ways but with the Qubit there is more choice of DNA and RNA kits available depending on the level of sensitivity required and the number of samples and you can also measure protein. Fluorescence-based technology is considered a more accurate method for quantification than the absorbance-based technology used by spectrophotometers such as the nanodrop. However, sample prep is more complicated and requires additional reagents, so fluorescence is usually only used when a really accurate measurement is required, such as for sequencing, cloning, protein assays, etc. Using the Qubit to measure protein concentration can be useful if you only want to use very small amounts or if the colour of your sample would interfere with a colorimetric method.

Users are responsible for purchasing their own reagents and preparing the tubes at their own bench, then transporting the tubes to the machine in 19AX02 to read the samples. 

Health and safety

CRA-1100 and 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 Qubit.

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

Serviced annually in accordance with the FHMS-wide centrifuge service contract.

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

This machine is covered by a service contract with Labtech, which includes an annual service visit by a qualified engineer.