*** Data Underlying:  Photodamage and Excitation Energy Quenching in PSII: A Time-Resolved Fluorescence Study in Arabidopsis ***
Authors: Cleo Bagchus, Herbert van Amerongen, Emilie Wientjes
Laboratory of Biophysics, Wageningen University & Research

Corresponding author: Emilie Wientjes

Contact information:
emilie.wientjes@wur.nl
Laboratory of Biophysics
Wageningen University & Research
Stippeneng 4, 6708 WE Wageningen
The Netherlands
Tel: +31317485129
www.wageningenur.nl/bip

***General Introduction***
This dataset contains the raw data underlying the article: 'Photodamage and Excitation Energy Quenching in PSII: A Time-Resolved Fluorescence Study in Arabidopsis'. In this research, the effect of photoinhibition on the fluorescence lifetime of PSII was determined for WT A. thaliana and chemically-treated/mutant A. thaliana. The effect of photoinhibtion was determined with both a streak-camera setup to generate picosecond fluorescence measurements and PAM fluoremetry with a Mini-PAM-II (Walz). The data was collected between February 2024 and April 2025.  For more details about the conducted research, we recommend reading the article associated with this dataset. The licence for this dataset is CC BY 4.0.



***Used Equipment***
The PAM fluorometry data was recorded on a MINI-PAM-II with the associated Win-Control software. The same samples were measured on a streak-camera setup. This system combines a pulsed laser source (Rock white light laser, Leukos) with a streak-camera detecting system (C10910, Hamamatsu). 

***Description of the Data in this Dataset***
The data in this dataset is separated according to the type of plant (WT, chemically-treated WT, mutant) and the type of data (raw streak data, streak data after analysis in glotaran, PAM data). 

The results after analysis in glotaran: 
- WT_results_Glotaran.zip: This folder contains the Glotaran output of the analysis of WT photoinhibition data. This output is the DAS and their associated fluorescence lifetime in separate .ASCII files. The fluorescence lifetimes are also summarized in an excel file. The name indicates the date of measurement, the duration of the HL treatment and the replicate. 
- var2_1_results_Glotaran.zip: This folder contains the Glotaran output of the analysis of var2-5 photoinhibition data. This output is the DAS and their associated fluorescence lifetime in separate .ASCII files. The fluorescence lifetimes are also summarized in an excel file. The name indicates the date of measurement, the duration of the HL treatment and the replicate. 
- var2_5_results_Glotaran.zip: This folder contains the Glotaran output of the analysis of var2-5 photoinhibition data. This output is the DAS and their associated fluorescence lifetime in separate .ASCII files. The fluorescence lifetimes are also summarized in an excel file. The name indicates the date of measurement, the duration of the HL treatment and the replicate. 
- chlorina_results_Glotaran.zip: This folder contains the Glotaran output of the analysis of chlorina photoinhibition data. This output is the DAS and their associated fluorescence lifetime in separate .ASCII files. The fluorescence lifetimes are also summarized in an excel file. The name indicates the date of measurement, the duration of the HL treatment and the replicate. 
- longterm_linco_results_Glotaran.zip: This folder contains the Glotaran output of the analysis of WT treated with lincomycin longterm photoinhibition data. For more information on the treatment, we refer to the paper. This output is the DAS and their associated fluorescence lifetime in separate .ASCII files. The fluorescence lifetimes are also summarized in an excel file. The name indicates the date of measurement, the duration of the HL treatment and the replicate. 

The streak images, shading- and background-corrected: 
- WT_streak_results.zip: This folder contains the shading-and background-corrected streak images of  the WT plants. The measurement conditions are indicated in the name.
- var2_1_streak_results.zip: This folder contains the shading-and background-corrected streak images of  the var2-1 plants. The measurement conditions are indicated in the name. 
- var2-5_streak_results.zip: This folder contains the shading-and background-corrected streak images of  the var2-5 plants. The measurement conditions are indicated in the name. 
- chlorina_streak_results.zip: This folder contains the shading-and background-corrected streak images of  the chlorina plants. The measurement conditions are indicated in the name. 
- longterm_linco_streak_results:This folder contains the shading-and background-corrected streak images of  the plants treated with lincomycin long-term. The measurement conditions are indicated in the name.  

PAM-data: 
- PAM_WT.zip: contains excel files (.xlsx) with the Fv/Fm values of the WT plants. The names of the files indicate the date (measuring conditions can be found in the streak name) or the measuring conditions.
- PAM_var2_1.xlsx: PAM Fv/Fm values of the var2-1 plant. 
- PAM_var2_5.xlsx: PAM Fv/Fm values of the var2-5 plants. Different sheets are the different measuring conditions. 
- PAM_chlorina.xlsx: PAM Fv/Fm values of the chlorina plant. 
- PAM_longterm_linco.xlsx: PAM Fv/Fm vlaues of the long-term lincomycin treated plants. Sheets are labeled with the data. 21-08-2024 data was a photoinhibitory treatment of 1h, while 21-08-2024 data was a photoinhibitory treatment of 2h. 
-PAM_data_recovery.xlsx: PAM data of the recovery after 4h of HL treatment in the presence of water or lincomycin (as different sheets) 



***Software to open Data in Dataset***
The .img files were corrected in the Hamamatsu software that runs the detection unit of the streak camera (HPDTA). These corrected images can be openend in the Glotaran software (https://glotaran.org/) or the specific python code for plotting these images. Data analysis of these images in the Glotaran software resulted in .ascii files of the DAS and the lifetimes associated with these DAS. These lifetimes are summarized in excel files. These can be opened with the associated python scripts. 

***Description of the Python Codes in this Dataset***
Python codes were used to analyse the data per mutant. This code imports .ASCII files of the DAS and the lifetimes associated with these DAS .ASCII files in an excel file. The output of the file are the PSI/PSII lifetimes (including the corrected PSII lifetime), together with the average DAS with the standard deviation. 

The following Python codes were used to analyse the data: 

-20250411_chlorina_remeasure_analysis.py to analyse the chlorina data 
- 20240801_streak_photoinhibition_FtsH_unmixing.py to analyse the var2-1 mutant data 
- 20241203_streak_photoinhibition_var2_5_unmixing.py to analyse the var2-5 mutants
- plot_streak_spectra.py to plot the streak spectra from the .img streak camera images 
- 20250303_analyse_streak_PSI_PSII_mixing_scatterplots. py to analyse the WT data 
- 20240801_streak_photoinhibition_longterm_linco_unmixing.py to analyse the longterm lincomycin-treated data 