Setting up the instrument for PCR (SYBR and TAQMAN) Base on ABI 7900 Book instrument Go to ‘www.mrl.ims.cam.ac.uk/intranet/booking/genomics/’ Clk the instrument you want 384 = ABI 7900 96 = ABI 7300 This takes you to the Google Calender Log in Click on the calendar slot you want Enter name and edit the time slot Start programe Clk ‘SDS 2.3’ Clk ‘Okay’ at the user identification page Select the following Assay: Standard Curve (AQ) absolute quantification Cond: 384 Well Plate Template: Blank Template Clk ‘Okay’ Select the detectors to use Clk ‘Tools’ then ‘Detector Manager’ Select the detector you want to use TAQMAN Reporter = FAM Quencher = TAMRA SYBR Reporter = SYBR Quencher = NA Clk ‘Add to plate document’: You can add more detectors if we use different detectors simultaneously Clk ‘Done’ Assign the detector to the wells you want Select the wells by dragging the mouse Assign the detector to use on the right hand pane Check that passive reference = ROX Instrument setup Clk ‘Instrument’ tab Clk ‘Thermal Cycler’ Check that Mode = Standard Sample volume = usually 12ul The cycling parameters are as above 9600 emulation is OFF For SYBR runs you need to add dissociation stage; this checks the purity of the amplification. If >1 product is amplified, there will be 2 peaks Clk the figure at the end of ‘Stage 3’ Clk ‘Add dissociation stage’ button at the bottom of the menu Connect to instrument and starting the run Clk ‘Real time’ Tab Clk ‘Connect to instrument’ Clk ‘Open/Close’ Load the plate in Clk ‘Open/Close’ Clk ‘Start Run’ Analysing the output Open SDS2.3 Clk ‘File’ For ABI 7900; D:/Applied_Biosystems/SDS Documents/Chong/xxx Select the wells you want to analyse Clk ►; 2 new tabs will appear ‘Result’ and ‘QC summary’ Look at the left pane Green colour = okay Yellow with numbers = error; 1 = empty wells/none detected Under the ‘Result’ tab, select ‘Amplification plot’ Look also at the results table on the bottom left Optimising the output Target CT values should be between 25 to 35 For 18s, the CT are usually very low because of high concentration of 18s The CT cutoff line (the green line) should be optimized Optimum cutoff should be across the most linear phase of the amplification The CT cutoff is different between different genes; each gene should be optimized separately The CT cutoff line should aim to avoid areas of noise Optimising the CT cutoff Select all the wells with the same gene Exclude empty wells and –rna wells Analyse the data If CT cutoff not optimize; Clk ‘Analysis Setup’ Adjust the baseline region; eg CT between 3 to 25. This tells the software where the baseline extend to Manual adjust allows you to manually move the line on the plot Export the results Clk ‘File’ Clk ‘Export’ Clk ‘Result table’ Clk ‘Selected wells’ Format SDS2.3; tick group by replicates Select location to save Disconnect instrument