Thermocyclers - Realtime PCR instruments - Liquid Handling Robots - Viaflo96 - Licor Odyssey- Qubit
Agilent RNA Bioanalyzer - BioRad Geldoc System - Sequenom Mass Spec System -Vilber_Fusion - ClarioStar - Qiagen DNA & RNA Extraction - Digital PCR Quantstudio 3D
Please have a look at our Document and Links webpage we have almost all software and instrument manuals for a quick download and often a link to the analysis sofwtare
We have a range of Thermocyclers in the 96 and 384 well format both gradient and non-gradient. From Applied Biosystems we have two Veritech instruments (modern version of the 9700 Geneamps), one 384 well the other 96 well format with linear gradient.
All our real-time instruments have 384 well blocks and can be booked via the Garvan booking system.
There are three LightCycler 480s (Roche), two ABI PRISM 7900 HTs (ABI) and one Biorad C1000 available
Each instrument is charged $50 per two hour slot of usage.
LightCycler 480 Technology
PCR specificity and yield are directly related to the ability of the thermal-cycling system to rapidly and accurately arrive at and maintain reaction temperatures. To achieve the superior performance in 384-well format, a new type of thermal block cycler was integrated into the LichtCycler® 480 Real-Time PCR System. Heating and cooling is achieved using Peltier elements.
Additionally, the novel thermal block cycler incorporates Therma-Base technology for optimal heat transfer and distribution to all samples on a multiwell plate (see Figure below). The Therma-Base unit, located beneath the Peltier elements, ensures optimal heat distribution across the plate and, as a consequence, optimized well-to-well homogeneity as well as maximized inter-well assay reproducibility. The cooling element below the Therma-Base unit features a maximized inner surface area to facilitate rapid heat absorption.
Figure 1. LightCycler 480 384-well thermal block cycler (left) and cross-section showing the integration of the Therma-Base (right).
The Therma-Base is based on evaporation and condensation of a working fluid in a thin vacuum chamber enabling rapid heat distribution and temperature equilibration.
The LightCycler 480 System I instrument can be booked 24/7 for high throughput realtime analysis ("GMG_LC480_1313" on the Garvan booking system), the instrument is housed in room 8.01 on level 8 of the Garvan building.
This instrument has a silver block and optimized optics for even higher accuracy when performing HRM (High Resolution Meltcurve) analysis. So when you consider performing SNP-analysis via HRM, this instrument is the first choice. This instrument can be found in the main Garvan Molecular Genetics facility room, room 8.02B in the Garvan building.
The software to analyse your data will work only on a PC and can be downloaded from the Pandora server via:
- \\Pandora\Volumes\Software\Windows\GMG_Software\LightCycler480 \LightCycler480_Software_Setup.exe
There is an additonal word document that contains the password and installation instructions under:
ABI PRISM 7900 HT Technology
The ABI PRISM 7900 HTs are our working horses in the facility, booked day and night and already set up for convenient Taqman assay analysis. Additionally the ABI PRISM7900 HT from ABI can be used with the Micro Fluidic Card block allowing for performing runs with predesigned assays from Applied Biosystems for which the facility houses all necessary adaptors and calibration cards, please check out the "TaqMan Low Density Array" at Applied Biosystems for more information.
Figure 2. The TaqMan Custom Array is a 384-well micro fluidic card that enables researchers to perform 384 simultaneous real-time PCR reactions without the need to use liquid-handling robots or multichannel pipettors to fill the card.
This low- to medium- throughput micro fluidic card allows for 1-8 samples to be run in parallel against 12-384 TaqMan Gene Expression Assay targets that are pre-loaded into each of the wells on the card.
The TaqMan Custom Array is completely customisable. A minimum order of 10 cards is required for all formats (TaqMan Low Density Array).
There are two ABI PRISM7900 HT instruments which can be booked 24/7 on the Garvan booking system. These instruments are designed for high throughput realtime analysis ("GMG_7900_2831" and "GMG_7900_3091"). Both instruments are housed in the Garvan Molecular Genetics facility on level 8 of the Garvan building in room 8.01.
The software to analyse your data will work only on a PC and can be downloaded from the Pandora server via:
- \\Pandora\Volumes\Software\Windows\GMG_Software\SDS 2.3 revA Installer.exe
There is no setup or password needed for the software.
The latest acquisition for realtime PCR is the QuantStudio 7 which can be booked 24/7 on the Garvan booking system. This instrument is designed for high throughput realtime analysis ("GMG_QuantStudio7"). The instrument is located in the Garvan Molecular Genetics facility on level 8 of the Garvan building in room 8.01.
The software to analyse your data will work only on a PC and can be downloaded from the internet, please click on the link:
The Biorad C1000 is the latest acquisition in the Garvan Molecular Genetics facility, its light source is LEDs hence it is small in size compared to the older instruments. The instrument can be found in room 8.01 in the Garvan building. Booking on the Garvan booking system under "GMG_BioradC1000", the instrument charge is $50 per run.
The latest acquisition for digital PCR is the QuantStudio 3 which can be booked 24/7 on the Garvan booking system("GMG_QuantStudio3D"). The instrument is designed for absolute quantification, Copy Number Variance (CNV) and Next Gen Sequencing library quantification. You can run Taqman assays with this instrument or you can use SYBRgreen based assays. The instruments is located in the Garvan Molecular Genetics facility on level 8 of the Garvan building in room 8.01. All reagents including chips for performing digital PCR can be purchased through the facility (please have a look in our Garvan Molecular Genetics Shop).
The software to analyse your data will work on a PC and Mac and is cloud based, please click on the link:
Please have a look at our Document and Links webpage for further links to manuals and helpful documents.
The Quantstudio 3 can be used for precisely quantifying NGS library preps. There are 3 different Taqman assays (part number 4331182) which are used for the different Illumina NGS kits:
- For the Illumina® Nextera Library Quantification Assay use TaqMan® Assay ID Ac04347696_a1
- For the Illumina® TruSeq DNA/RNA Library Quantification Assay use TaqMan® Assay ID Ac04364396_a1
- For the Illumina® TruSeq Small RNA Library Quantification Assay use TaqMan® Assay ID Ac04347697_a1
More information on using Digital PCR to quantify NGS libraries:
There are three liquid handlers for PCR setup at Garvan Molecular Genetics. The PCR setup instruments are EPmotions, two 5070s with 4 deck positions and one 5075 with 12 deck positions. (Please find a manual and a programming SOP for the EPmotion robots here).
The ease of programming pipetting steps with the ep-blue software of these instruments in particular has led to their predominant usage in research laboratories in Europe and Australia. The operator can drag and drop with some mouse clicks very intuitively where from (source) and where to (destination) so that high throughput 384 well pipetting is made easy and fast.
Additionally the EPmotions operate with pipetting tools that are identical to hand-held pipettes therefore adding accuracy to the precision of the automation. These are some screen shots from the ep-blue software illustrating the simplicity of the process:
There are two 5070 EPmotions, one for the cancer research groups and one for all other research groups. The instruments can be booked on Garvan's booking system under "GMG_EPmotion_Cancer" and "GMG_EPmotion_All Groups". There is a charge of $30 per 384plate setup (approx 2h).
We have also a large PCR setup robot which has 16 deck positions and is mainly used for mouse genotyping PCR setup but we can setup qPCRs for large scale projects too, you would submit samples and pay a per PCR plate well price, come and talk to us.
The Sequencing Service Coordinator maintains and operates the sequencing instruments in the facility, the ABI 3130XL and ABI 3500 sequencers, which have 16 and 24 capillaries and processes ~ 30,000 samples/year. We operate 50cm arrays giving up to 1000 bases read length in 2.5h.
For RNA and DNA analysis the facility houses a Bioanalyzer from Agilent with the capacity to analyse 12 samples on one chip. The instrument is maintained by the facility staff and RNA Nano, RNA Pico, DNA 1000 and DNA HighSensitivity chips + reagents can be purchased from us (please see Molecular Genetics shop for prices). We will train you on the instrument and you are free to book the instrument on Garvan's booking system ("GMG_Agilent_2100"). Find manuals for operation of the instrument and the kits for download on our Document and Links webpage. The instrument is located on level 4, Garvan, in room 4.02.
For DNA analysis the facility houses the Biorad Geldoc system with the capacity to document and export to JPG-format protein, DNA and RNA gels (alternatively there is the E-box system in TKCC level 8, grey room). There is are "How to do"- Instructions attached to the side of the instrument for quick setup. For all non-ordinary questions facility staff will kindly assist you. For operation of the Geldoc system you are required to wear gloves for safety reasons as the area is potentially contaminated with Ethidium Bomide. Find an operation SOP and a safety SWP (Safe Work Procedure) for the BioRad Geldoc System for download on our Document and Links webpage. There are also alternatives for Ethidium Bromide as intercalating dye which you can find in our Molecular Genetics shop. Analysing your gel photos is possible most conveniently with analysis software installed on your computer. The Fusion Fx7 software and the E-Box software can analyse gel photos even if they are not originally taken with the Fusion or E-Box, please have a look at our Document and Links webpage for the links to the software.
For DNA and RNA quantification the facility houses a Qubit fluorometer. We also sell the DNA Broad Range, DNA High Sensitivity and RNA High Sensitivity kit reagents (you pay per samples measured). Please have a look on our Molecular Genetics shop webpage for prices and download the manual from our Document and Links webpage.The system is located on level 8 of Garvan room 8.05 and does not require booking.
The Methylation and SNP-Genotyping Coordinator maintains and operates the Sequenom Mass Spec system which is compromised of the Mass Spec and the Nanodrop liquid handler. The facility offers both, a service for methylation quantification or SNP genotyping samples and usage of the system after completion of training.
The Qiacube Robot at the Molecular Genetics Facility enables high quality DNA and RNA extraction based on columns. The plug-and-play instrument runs all Qiagen spin-column kits currently on the market (but only Qiagen kits, no competitior products will work).
12 samples can be processed at once and one run takes about 45 minutes. The faciltiy provides DNeasy (normal blood and tissue extraction) and Investigator (high sensitivity extraction) kit columns to be purchased. All other kits (like RNA extraction etc) can be ordered but are not readily available. The instrument is called "GMG_QiaCube" on Garvan's booking system, the instrument is located in room 8.02A (Garvan).
Alternatively you can use Garvan Molecular Genetics' DNA extraction service. This service extracts your DNA or RNA from tissue, blood, FFPE, Serum, Cells and other materials. We use a QiaSymphony for this automated high throughput extraction service.
The Viaflo96 semi automated pipetting aid enables liquid transfers in the range of 1ul to 125ul in the 96well format. This liquid handler can be programmed like a robot and will perform transfer steps from 96 and 384well plates to 96 and 384 well plates. It operates in the same way the Viaflo single and multichannel electric pipettes are operated.
The instrument is used for our Sequencing Service but can also be booked on the Garvan booking system as "GMG_96Viaflo" outside peak hours. The instrument is located in room 8.05 (Garvan).
The Fusion FX7 has the same or better sensitivity than conventional chemi-luminescence detection systems (films), it comes with the following specs:
- 7 excitations channels options in the IR, NIR, visible RGB and UV area
- 10 Spectra narrow band filters available from 440 to 850nm
- 2,048 x 2,048 pixels resolution,16-bit (65,536 grey levels) with integration time
- Fixed focal length motorized lens (f. = 0.84) with Autofocus
- Motorized 6-position Filter slide with F-590 filter
- Darkroom with white-light epi-illumination and 20.M UV table
Please click here for more information like protein ladders that show up in the chemi-luminescence blot. Please click here for the manual of the instrument. The Fusion Fx7 is located on level 8 of TKCC in the grey room. The instrument is called "GMG_FusionFx7" on Garvan's booking system, the booking slots are 30min, you need to cool the camera down first which will take 5min. You can take your images on the Fusion Fx7 as is explained in the training video and analyze them at your desk with a free software which you can download via the following link (both Mac/PC): image_studio_lite_software.
The Li-Cor Odyssey was purchased to address all Western blot documentation needs. Antibodies and Blocking buffer are sold in Garvan Molecular Genetics Shop. The following membranes are suitable/compatible for western blots on the Odyssey system:
- PVDF-FL (Immobilon-FL)
- all brands of Nitrocellulose
Please note: Standard PVDF (immobilon-P) is not compatible with the Odyssey system. You can take your images on the Odyssey system and analyze them at your desk with a free software which you can download via the following link (both Mac/PC): image_studio_lite_software. There are useful pdf documents about the Infrared dye, quick setup and troubleshooting in our Documents and Links site. The system is located on level 8 of TKCC in the grey room and does not require booking. The Li-Cor Odyssey is located on level 8 of TKCC in the grey room. The instrument is called "Licor Odyssey Clx Asset 8547" on Garvan's booking system.
The The CLARIOstar is a multifunctional microplate reader capable of performing a wide array of applications for fluorescence intensity, fluorescence polarization, time-resolved fluorescence, TR-FRET (e.g. HTRF®), luminescence, AlphaScreen®, and full spectrum absorbance.
- Spectral Range: 340 - 740 nm (selectable increments of 0.1 nm)
- High-energy xenon flash lamp
- Dedicated Laser for AlphaScreen® / AlphaLISA®
- 6- to 1536-well plates, LVis Plate with 16 microspots (2 μL)
- Fluorescence Intensity - including FRET
- Luminescence (flash and glow) - including BRET
- UV/Vis Absorbance
- Fluorescence Polarization / Anisotropy
- Time-Resolved Fluorescence - including TR-FRET
- AlphaScreen® / AlphaLISA®
The analysis software and operation manual can be found on our webpage Documents and Links site. The system is located on level 8 of Garvan room 8.01. The instrument is called "GMG_ClarioStar" on Garvan's booking system.