Data_Code_Reports_Trives_et_al_2024

Social Experience is Associated with a Differential Role of Aromatase Neurons in Sexual Behavior and Territorial Aggression

What's in this repository ?

This repository contains data analysis reports together with the code (R) and raw data used in the paper: Social Experience is Associated with a Differential Role of Aromatase Neurons in Sexual Behavior and Territorial Aggression (Trives, Porte, Nakahara, Keller, Vacher & Chamero, 2024). All the results presented in the paper can be reproduced by running the corresponding R markdown file (use R studio to open and run it).

How is it organized ?

The main folder Data_Code_Reports_Trives_et_al_2024 contains 3 sub folders as follows :

• Data Analysis Reports: contains all the html reports which include code and outputs containing all the data analysis workflow for all the figures in the paper, together with descriptive and inferential statistics (mean, sd, n, proportions, statistical tests, p-values...).

• Behavior:

  • Extracting_Raw_Behavioral_Data: This folder contains all the raw ethograms generated by blindly and manually annotating video files with the software Boris (Friard et al. 2016). Meaningful behavioral data (durations, latencies...) have been extracted from these raw ethograms with the code available in the corresponding R markdown file. Two .csv files containing all the meaningful behavioral data from all animals are generated as the output of this step (one file for each behavior (sex vs aggression)).

  • Analysing_Extracted_Data: This folder contains the code and raw data to generate all the analysis done for Figure 1 and Figure S1 of the paper. The code is formatted in an R markdown file that you can open with R studio. The analysis is split in three subfolders, one for behavioral parameters (Fig.1C right & Fig.1D right), one for proportions (Fig.1C left & Fig.1D left) and one for training data (Fig S1). All of these steps are performed on the outputs generated from the extraction of the raw behavioral data.

• Histology:

  • Extracting_Histology_Data: This folder contains data obtained from confocal images of the respective brain regions stained for Egr1 and Hoechst (Figure 2 et 3) and mCherry (Figure 4). First, the images have been z normalized using the python script available in the folder Normalization_Images and then loaded in the software QuPath (Bankhead et al., 2017). Regions of interest (each brain region) have been manually annotated and cells were detected based on the Hoechst staining in each ROI. The output of this step is a table containing fluorescence values for each detected cell and in different cell compartments (nucleus, cytoplasm, total) for the different color channels (blue, green, red), for each slice and each animal. This raw output from qupath is included in each brain region folder. The code used to add meta data and compute the proportion of Egr1+ or mCherry+ Egr1+ or mCherry- Egr+ is formatted in an R markdown file in each brain region folder. For each region, a .csv file containing the corresponding proportions for each animal and the meta data is generated. Importantly : the file generated for the MeA contains other brain regions (Arc, DMH, VMHvl, VMHc, VMHdm) presented in Figure S2. They are indicated in the column "Parent".

  • Analysing_Extracted_Histology_Data: This folder contains the code and raw data to generate all the analysis done for Figure 2, 3 and 4. For the code, you will find 1 R markdown file for the analysis of each figure separately. The code takes the data located in the folders "res_final" (Figure 2 et 3) and in "res_final_mCherry" (Figure 4) which are the .csv files generated from the extraction of the histology data in the previous step.