Name all gels when they are generated with a descriptive name that includes the data.
Copy Gel images from Chemidoc to server.
Copy Gel images from server to local device for analysis. Copy and paste twice to make sure that raw file is not accidentally edited in the process of making the pretty version and the analysis version.
Keep directory names and file names descriptive.
Making Pretty Version of Figures
Open up copy of file in Image J.
Crop to region of interest.
Adjust contrast (Under Image > Adjust > Contrast). Mainly focus on adjusting the minimum and maximum contrast.
Save file as both a TIFF and a JPEG (Do not over write the raw TIFF!!!). Include “pretty” (or “forFig”) in file name before the extension.
Data Analysis of Gel Images
Open up copy of file in Image J.
Crop to region of interest.
Subtract Background (Under Process > Subject Background > Check “Light background” if data is black bands on light background)
Save file as TIFF with for analysis in file name before the extension.
Set Measurements (Under Analyze > Set Measurements). Make sure “Integrated Density” is checked.
Create a band box that is as big as the biggest band. Make sure that the band box size is not changed during analysis. Make sure to only change X position when analyzing different lanes.
Measure band intensity (Under Analyze > Measure or Ctrl + M or Command + M). Also measure the background at three random places and take the average for background subtraction.
Transfer “Integrated Densities” to Excel and perform appropriate data analysis.
