Documentation:Standard Operating Procedures for Densitometer

Please obtain proper training from the FNH education and research technician Imelda Cheung (Imelda.Cheung@ubc.ca) prior to using the Densitometer.
- A video at https://youtu.be/eonBbU-IGzk is also provided for review purpose and can be viewed as needed.
To scan the gel:
1. Place your gel on the scanner surface. Make sure that the gel is straight so that the bands are easy to analyze. Orient gels such that the resolving gel for SDS PAGE or the cathode side of the IEF PAGE gel is at the top of the gel. Close the lid of the scanner.
2. Open up “LabScan”.
3. Click on the icon of the “scanner with a question mark” (this is a preview scan).
4. Once a photo of your gel appears, click the “crop tool” icon and draw a square around your whole gel.
5. Next, click the icon of the “scanner with no question mark”. This will take a picture of only the area inside the square that you created.
6. Click the “save” button and save your photo as a .tiff file by selecting the option from the drop down menu. Save your photo under your lab group number and the type of gel (SDS or IEF). Note where on the computer your photo is saved. It should automatically be in the “LabScan” folder but this may not always be the case.
To convert file type:
1. Open “IQTL calibration converter”. This program will convert your image such that the bands can easily be detected by the analysis program.
2. Click “add file” and select your saved .tiff photo of your gel.
3. Click “convert file”. It should notify you that the conversion was successful.
To analyze the image:
1. Open “Image Quant TL”.
2. Click “1D gel analysis”.
3. Select the converted photo file that you created. It will appear as your file name followed by “(IQTL)”. Click open.
4. To edit lanes:
  1. Click “stepwise” from the left side panel within the software. Then select the “parameters” tab.
  2. Click the “manual” icon and change the number of lanes to number you want to analyze on your gel.
  3. Click and drag a square area on your gel photo, the square should also include the number of lanes that you specified in the previous step.
  4. Select “edit single lanes” from the drop down menu. You can also select “edit multiple lanes” if you wish to make all lanes longer or wide etc.
  5. Click on the move or bend icons to re-frame your lanes accordingly such that all bands are included.
  6. When finished, click the “next” arrow.
5. To subtract background:
  1. Click on the “parameters” tab again.
  2. Select the “image rectangle” option.
  3. Create a rectangle on the gel photo that represents an area of the gel where bands are not present. This is your background colour which will be subtracted from the colour of your bands.
  4. When finished, click “subtract” and then the “next” arrow.
6. To select band:
  1. Click the “detect” icon then begin to manually select and trim your band widths. To add additional bands not detected by the program, simply left click in the middle of the band. To trim the width of the bands use the window on the right side of the software screen.
  2. When you have finished selecting your bands, click the “next” arrow.
7. To perform molecular size calibration:
  1. Select the “parameters” tab and then from the drop down menu select “TH Mar 2017 SDS” or “TH Mar 2017 IEF” standard.
  2. Next assign a standard lane by left clicking on the lane corresponding to the standards. A yellow box should appear around it.
  3. Click “compute”. A graph will appear showing the standard vs. the distance travelled on the gel. The resulting curve is logarithmic so you will need to export your data to excel for further analysis.
  4. At the top of the screen click “edit” then “export to excel”. Save your file to usb using your group number and the type of gel. You should also save and take with you a copy of your converted gel photos (IQTL) to include in your report.