Representative dataset of radiation and drug treated GEDI expressing SF8628 cells and FIJI & R scripts for GEDI ratio quantification and plotting
There are currently 2 image datasets that can be shared via email request (voza@uky.edu) (a better open cloud storage option is being worked on):
- SF8628-GEDI expressing cells that have been treated with 25Gy and imaged for 8 timepoints (T0-T7) [SF8628_50uM_JQ1_Image_dataset.zip]
- SF8628-GEDI expressing cells that have been treated with 50uM JQ1 and imaged for 7 timepoints (T0-T6) [SF8628_50uM_JQ1_Image_dataset.zip]
Each dataset has a 2 scripts associated with it: A) A Fiji script that can be used to threshold and quantify mApple and GC150 intensities. Currently the script can only be run on 1 image file at a time. There are 2 FIJI scripts for each dataset 1) GEDI_002_Fiji_Script_JQ1_50uM.ijm 2) GEDI_003_Fiji_Script_25Gy_Timelapse_20X.ijm
Thresholding values are suggested/recommended.
B) An R script that can be used to compile CSVs from all timepoints that are from the FIJI script output and calculate GEDI ratios for each object. The R markdown file is titled [BIND_FIJI_CSVs.Rmd] The working directory where all the CSVs are located will have to be changed accordingly
Size filters that have been used after FIJI and R analysis in the associated io.protocol are as follows: Area: 2500-30000
There are 2 sets of CSV files that are the FIJI output from each imaging dataset (25Gy and 50uM JQ1) and have been run using the uploaded FIJI scripts and can be directly inputed into the Rmd file. 50uM JQ1 CSV output from FIJI is titled [GEDI_JQ1_50uM_TImeSeries.zip] 25 Gy CSV output from FIJI is titles [FIJI_Output_GEDI_25Gy_TImeSeries.zip]