Using the zoom adjustment, zoom on the gel Adjust the tray on the VGAU 3000 to see the image of the gel in the viewfinder

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Operation of Vakili 3000 Gel Analysis Unit Both qualitative and quantitative analysis of electrophoresis experiments can be accomplished by using the Vakili 3000 Gel Analysis Unit.

Follow the step by step instructions below to create a report of your analysis.

1 Operation of Vakili 3000 Gel Analysis Unit Both qualitative and quantitative analysis of electrophoresis experiments can be accomplished by using the Vakili 3000 Gel Analysis Unit. There are three steps necessary to analyze the electrophoresis image: obtaining the image of the gel, enhancing the image of the gel, and analyzing the enhanced image. Follow the step by step instructions below to create a report of your analysis. Obtaining the Image of the Gel Place the gel on the tray Turn on the Vakili 3000 Gel Analysis Unit (VGAU3000) by turning on both the power key on the unit for camera and the light Double click on the VGAU 3000 icon on the desktop after inserting an electronic access key. From the file menu select New Experiment A window will appear asking if you would like to search for an image or acquire a new image. To acquire an image of your gel/sample click on acquire. If you already have a gel image, then use the browse option. In this case escape to Step 2. Click Connect to access the remote camera Set the Size/Quality of the image to Medium l/superfine In the shooting mode adjustment tab select the following settings. o Flash: Auto/Off o White Balance: Fluorescent o Exposure Compensation: Set to obtain best lighting. About +1 2/3 o Flash Exposure Compensation: Set to obtain best lighting. About +1 2/3 o ISO: 200 or Auto In the Angle Adjustment tab select the following settings. o Macro: On o Turn the viewfinder on Using the zoom adjustment, zoom on the gel Adjust the tray on the VGAU 3000 to see the image of the gel in the viewfinder Intermediate Biochemistry II / Methods in Biochemistry. Laboratory Manual,

Once you have a perfect image click on the Release Button to capture your image. Take a note of the image number. The images are saved in the image folder on the desktop.

2 Once you have a perfect image click on the Release Button to capture your image. Take a note of the image number. The images are saved in the image folder on the desktop. Close the imaging application, the image of the gel will be transferred to the VGAU 3000 software. If for some reason the transfer of the image dose not occurs, browse for the image and select it from the Image folder on the desktop. A window will ask you to save the experiment. Assign your locker number as the file name and save it in the folder called Gel reports on the desktop. Starting an Experiment Once the image is loaded, you ll see an image displayed in the preview window as follows: Complete the requested information on the experiment section. Enhancing an image Once an image is loaded in the image box, the Image Adjust menu will become active. From here, you can click on the Image Adjust menu and select the desired settings you want apply to your image. Intermediate Biochemistry II / Methods in Biochemistry. Laboratory Manual,

Drop down Menus Invert Contrast Brightness Rotate Allows you to Invert the colour s of the image To adjust the contrast of an image by adjusting the slider.

3 Drop down Menus Invert Contrast Brightness Rotate Allows you to Invert the colour s of the image To adjust the contrast of an image by adjusting the slider. To adjust the brightness of an image by adjusting the slider. To rotate an image by 90 degree s right Adjust the sliders on the pop up menus to your desired settings. Click OK Contrast Control Brightness Control Once you have completed enhancing your image (and/or saving the image), proceed to step 3. A reminder: It is a good idea to save your experiment several times during the analysis of your gel/sample. Select Save from the File Menu. Analyzing the Image Double click on the image where you like to select the front line of the gel/sample. You can also select the end of the lane where the dye traveled to by double clicking on the image again. Use the undo button if you have to make an adjustment. Intermediate Biochemistry II / Methods in Biochemistry. Laboratory Manual,

4 To select a lane, click and drag the left mouse button to select the area to be analyzed. A red rectangular box will show the area being selected. When the desired area has been selected, let go of the left button mouse to complete the lane selection. To analyze the selected lane, click on the Graph Selected Lane button. A graph window will then be displayed on the right hand side of the image box. Note: Once a lane has been graphed, the Image Adjust menu will become disabled and you can no longer adjust the image Setting a baseline To create a baseline, click once to mark the start of the x y coordinate and then drag a green line across the base of the graph. When the end of the x y coordinate is reached, click again and move the mouse pointer. A green line should be drawn across from the start to end of the selected x y coordinates. To create additional baselines, repeat the Setting a baseline procedures You can also resolve your picks by double clicking on the graph where you desire to resolve your picks To clear the last created baseline or peak resolver, click the Clear Baseline or the Clear the Peak Resolver button. Intermediate Biochemistry II / Methods in Biochemistry. Laboratory Manual,

On the bottom right of the screen, enter the Sample Name/Number and the Sample Description.

5 Once all of the baselines and peak resolver(s)for the graph have been entered, click on the Calculate Results button. A Lane x tab will appear at the bottom left of the screen displaying Sample Lane Statistics. On the bottom right of the screen, enter the Sample Name/Number and the Sample Description. If this lane is your Standard sample, check the standard box, and then type in the Molecular Amount (MA) and/or Molecular Weight (MW) values in the appropriate rows and columns. (This is Not Applicable to 3503 Lab) Repeat the above steps to analyse all the applicable lanes to your experiment. Note: Do not analyse your crude extract lane. Intermediate Biochemistry II / Methods in Biochemistry. Laboratory Manual,

6 To view different lane data, click on the appropriate tab menus. If the distances in the Sample Statistics box are not in a proper order, click on Distance to sort your data. A reminder: It is a good idea to save your experiment several times during the analysis of your gel/sample. Completing the Experiment and Printing To complete an experiment, click on the Generate Report button. A window will inform you that your report is generated and it is ready to print. Click OK and select Print from File menu. You can also preview your report by selecting Print Preview from the File menu. This computer has Adobe Acrobat. If you wish to generate a.pdf version of the report select Adobe Acrobat as your Printer during the Print process. To shut down the VGAU 3000, close all the applications and turn off the light and the camera on the VGAU3000 unit. Remove your gel from the tray and clean up the area. Intermediate Biochemistry II / Methods in Biochemistry. Laboratory Manual,

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