1. Getting Started on the Rotor-Gene-6000
Jennifer McMahon, PhD
corbett
LIFE SCIENCE

2. the world’s only real-time rotary thermo-optical analyser
Turning to instrument design, this brings us to the Rotor-Gene, the worlds only centrifugal thermal analyser.
Here we’re looking top-down at the open lid of the Rotor-Gene showing the rotor in position in the reaction chamber.
If you look carefully you’ll see tubes arranged under the silver locking ring in a circular configuration, similar to a centrifuge.

3. Cross-section of rotary optics
Reaction Chamber
Detection Filters
Lens
PMT Detector
Assembly
Spindle/Motor Assembly
Tubes Spin in Rotor (Red)
LED Light Source Assembly
To better understand centrifugal design, let’s look at an x-ray cross section view through the middle of the RG.
Click 1: Firstly, here’s the reaction chamber, a light-sealed unit, the top half of which swings open with the RG lid.
Click 2: Now here’s the rotor in position (here colored red). This is a 36-well rotor holding the largest tube type (0.2 mL). This makes it easier to see the individual tubes.
Click 3: This allows the tubes to spin around and pass the optic subsystem, which we’ll look in a moment.
Click 4: The rotor doesn’t hang in mid air as shown, it sits on a motorized spindle assembly, just like in a centrifuge.
Click 5: The light source is an array of individual LEDs (light-emitting diodes) arranges in a “gattler” assembly. The gattler turns to allow individual LEDs to be used as appropriate. There are up to 6 LEDs depending on the model.
Click 6: Detection of optical signals is via a photomultiplier (PMT), positioned at the side of the unit.
Click 7: The Detection subsystem contains a lens
Click 8: And a set of up to 6 filters, depending on the model.
Click 9: To detect signals, the selected LED illuminates each reaction as it spins past with a high-power burst of light.
Click 10: The reaction emits fluorescent energy…
Click 11: …which is focussed through the lens, passes through the selected filter and is detected by the PMT and reported.
It’s important to note that each tube is moved to the identical optical pathway. This simply means that there is no optical variation at each tube position. This is why the RG does not require any optical callibration, as other systems do.
Click 12: The RG is heated and cooled by fast-moving air. Even when collecting fluorescent signals the air in the chamber is circulating around each tube as they spin past the detector.
This ensures well-to-well thermal variation is absolutely minimal—below detectable levels in fact. Contrast this with other systems that typically suffer one degree or more difference across the block, particularly in edge wells.
To complete our understanding of the mechanism, vents are opened and cool air is imported through the base of the chamber and hot air is expelled through the top of the chamber (and out the vents on the lid) when the instrument is in cooling mode (not shown)
When heating, the chamber seals and an overhead heating element (not shown) raises the temperature of circulating air.

4. Click on Rotor-Gene icon
Getting Started……
Click on Rotor-Gene icon
Click on advanced tab for step by step run set up 
Choose run template depending on chemistry
Dual labeled probes = hydrolysis probes
SYBR = intercalating dyes

5. Select the rotor you are using, put the rotor into the machine with the locking ring attached
The locking ring tick box must be ticked to proceed
Click “Next”

6. Insert user name, any notes (primer conc, primer sequence mix used etc) and volume required (10-25uL)
This info is saved and can be printed in reports
Click “Next”

7. click on “Edit Profile” to change run parameters
section to be altered is greyed out, click on “Hold Temperature” to change temperature, click on “Hold Time” to change time 
Always read manufacturer’s instructions regarding Hot start Taq activation times

8. Click on “Cycling” to adjust the cycling parameters
Default cycle number is 40
To change a step click on the temperature and adjust then click on the time and adjust

9. Data is acquired each cycle (blue dots)
No blue dots = no data = very bad
Acquire at the end of the extension phase
Click on “Aquiring to Cycling A” to select colours
Move the colours you want from “Available Channels” to “Acquiring Channels” using arrows
Use Green channel for SYBR green

10. With SYBR use “Melt” to look for primer-dimer or non-specific product
Melt should start from acquiring temperature
If you start the melt from annealing temp the melt may have a shoulder on it
Use default settings, make sure you are acquiring data (blue dots)

11. Gain can be compared to the aperture on a camera and is used to fit data on raw scale
If your starting fluorescence signal is weak the gain should be high, if strong the gain should be low
Many people just accept default gain and go to “Next” on this screen, others optimise the gain for each run
Click on “Gain Optimisation” to begin

12. Click on “Optimise Acquiring” and “Perform Calibration Before 1st Acquisition”
If you have different colours in different positions click “Edit”
The colour you want to use must be in the tube position for calibration to be successful
Don’t set gain on no template controls

13. Click on “Start Run”
Save file name in directory of your choice 
Default nomenclature has name of template file, date and version (1 for 1st run that day etc)

14. To save as a template open template folder C:\Program Files\Rotor-Gene 6000 Software\Templates and save as template file (*.ret)
Run files are *.rex

15. Choose to enter sample names now or click “Finish” and enter sample names later
Run will commence, while the experiment is running you will see:
Raw Channel - fluorescence collected cycle by cycle
Temperature - profile as temperature cycles
Profile Progress – tells you time remaining, shows you where you are. “Skip” allows you to skip to next step (e.g. from cycling to melt); “Add 5 cycles” lets you add cycles at the end

16. Adding sample names and types
Can highlight blocks of cells for naming etc (like excel)
Samples with the same name will be treated as replicates regardless of position
Type can be standard, no template control, unknown (sample)
Click on “Edit Samples” on RHS of screen

17. Drop down “Type” menu to view options
If you choose “Standard” you have to add a value for concentration
If you are running two standards define one set on page 1 then make a new page (page 2) to define the second set of standards
Groups can be used to define e.g HKG (housekeeper) and GOI (gene of interest

18. Can choose colour from palette and can set colour gradient across range of samples/standards

19. Post run analysis - basic
Raw data is displayed on screen during the run and at the end of the run.
Analysis is needed to correct for background etc
Click on “Analysis” on the main toolbar at the top
Click on “Quantitation” tab
Click on channel so that it gets greyed out
Click on “Show”

20. The software looks at the standards and draws a threshold, calculates the standard curve and the replicates

21. “Dynamic Tube” normalisation should be on to correct for background
“Slope Correct” should be on for dual labeled probes
“Ignore first” can be useful if the first few cycles are different (usually higher) than the rest of the run

22. Dynamic Tube Normalisation
This option is ticked by default and is used to determine the average background of each individual sample just before amplification commences. Standard Normalization simply takes the first five cycles and uses this as an indicator for the 'background' level of each sample. All data points for the sample are then divided by this value to normalize the data. This process is then repeated for all samples. This can be inaccurate as for some samples the background level over the first five cycles may not be indicative of the background level just prior to amplification. Dynamic Tube Normalization uses the second derivative of each sample trace to determine a starting point for each sample. The background level is then averaged from cycle 1 up to this starting cycle number for each sample. This method gives the most precise quantitation results. Alternatively with some data sets it may be necessary to disable the dynamic tube normalization. If this is the case the average background for each of the samples is only calculated over the first 5 cycles. If the background is not constant over the cycles before amplification it will result in less precise data.
Slope correct
The background fluorescence (Fl) of a sample should ideally remain constant before amplification. However, sometimes the Fl-level can show an increase or decrease due to the effect of the chemistry being run and produce a skewed noise level. The Noise Slope Correction option uses a line-of-best-fit to determine the noise level instead of an average, and normalizes to that instead. Turning on this option can tighten replicates if your sample baselines are noticeably sloped. This function improves the data when raw data backgrounds are seen to slope upward or downward before the amplification Takeoff point (CT). It is very helpful for runs when for example the FAM background is seen to creep upwards due to gradual probe autohydrolysis.
Ignore first
The first couple of cycles in a quantitation run are not usually representative of the rest of the run. For this reason, you may get better results if you select to ignore the first few cycles. If the first cycles look similar to cycles after them, you will gain better results by disabling this function, as the normalization algorithm will have more data to work with. You can ignore up to ten cycles.

23. Click on “Threshold” button
If there are no standards in the run you have to set the threshold manually.
Click on “Threshold” button
“Click to select the threshold height” comes up, move the line up or down to select the threshold
Do this in log scale
Linear scale view, click on “log scale” button to get log scale
Log scale view, click on “linear scale” button to get linear scale

24. Standards are plotted in blue, samples as red
Software calculates relationship value (R2) – ideally 0.99
Software calculates the efficiency out of 1
1 means 100% efficient or doubling every cycle

25. Software calculates “Rep
Software calculates “Rep. Ct” to get replicate Ct from triplicates (geometric mean)
Software calculates “Rep. Ct Stc” to get standard deviation for triplicates
Software calculates “Rep. Calc Conc.” to calculate concentration from a standard curve
Columns can be switched off by right clicking on grey bar and changing options
Table can be exported to MS Excel by right clicking on table text and choosing export to excel

26. Raw melt data can be viewed at end of run
Raw melt data can be viewed at end of run. Fluorescence decreases as temperature increases
The software plots a mathematical derivative to turn the raw data into a peak
Click on “Analysis” then highlight “Melt” then click “Show”