Presentation on theme: "Getting Started on the Rotor-Gene-6000"— Presentation transcript:
1 Getting Started on the Rotor-Gene-6000 Jennifer McMahon, PhDcorbettLIFE 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 ChamberDetection FiltersLensPMT DetectorAssemblySpindle/Motor AssemblyTubes Spin in Rotor (Red)LED Light Source AssemblyTo 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 lensClick 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 iconClick on advanced tab for step by step run set up Choose run template depending on chemistryDual labeled probes = hydrolysis probesSYBR = 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 proceedClick “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 reportsClick “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 40To 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 badAcquire at the end of the extension phaseClick on “Aquiring to Cycling A” to select coloursMove the colours you want from “Available Channels” to “Acquiring Channels” using arrowsUse Green channel for SYBR green
10 With SYBR use “Melt” to look for primer-dimer or non-specific product Melt should start from acquiring temperatureIf you start the melt from annealing temp the melt may have a shoulder on itUse 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 lowMany people just accept default gain and go to “Next” on this screen, others optimise the gain for each runClick 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 successfulDon’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 cycleTemperature - profile as temperature cyclesProfile 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 positionType 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 concentrationIf you are running two standards define one set on page 1 then make a new page (page 2) to define the second set of standardsGroups 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 etcClick on “Analysis” on the main toolbar at the topClick on “Quantitation” tabClick on channel so that it gets greyed outClick 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 correctThe 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 firstThe 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 thresholdDo this in log scaleLinear scale view, click on “log scale” button to get log scaleLog 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 0.99Software calculates the efficiency out of 11 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 triplicatesSoftware calculates “Rep. Calc Conc.” to calculate concentration from a standard curveColumns can be switched off by right clicking on grey bar and changing optionsTable 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 increasesThe software plots a mathematical derivative to turn the raw data into a peakClick on “Analysis” then highlight “Melt” then click “Show”
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