Size-dependent temporal decoupling of morphogenesis and transcriptional programs in pseudo-embryos

This repository contains data used to generate the results presented in Bennabi et al. 2024.

Detailed information about the individual folder content 

• sam_vit\_h\_4b8939.pth file:
  This file contains the pre-trained weights for the Segment Anything Model (SAM) with a Vision Transformer (ViT) backbone. This can be used to replicate the segmentation of gastruloid in brightfield timelapse movies for the morphological analysis.
  
  
  
• qPCR_ddct_analysis_actb.csv file:
  This file contains the RTqPCR data of the biological replicates 1 and 2, including the (Well_Position, Sample_Name, Target_Name, CT, etc.) that were used to generate the graphics in Figure S7 A and B. 
  
  
• Figure_1_S1-2:
  The content in this folder was used to generate the graphs for Figure 1 and the corresponding supplementary Figure S1 and S2. It is split into two main sets of images and data.
  • Included:
    • a Figure_1_movies folder containing brightfield timelapse images of gastruloids for different size conditions in batch 2.
    • a Figure_1_dataframes folder containing the preprocessed dataframes to all analysed movies that can be directly used to recreate all graphs in Figure 1 and S1-2.
  • Not included:
    • live movies of gastruloids for batch 1 and 2
    • movies and dataframes classified as outlier (excluded from the analysis)
      
      
      
• Figure_2_S3
  The here provided data can replicate all all graphs of Figure 2 and the corresponding supplementary Figure S3.
  It is sorted into two seperate sets of images and data.
  
  • Included:
    • a Figure_2_movies folder containing 25 live movies of Mesp1/2 gastruloids for different size conditions. per size condition.
    • a Figure_2_dataframes folder containing the preprocessed dataframes to all analysed movies that can be directly used to recreate all graphs in Figure 2 and S2.
    • a configs folder with the configs.yml file specified to facilitate the multipolarity analysis from the dataframes provided in Figure_2_dataframes.
  • Not included:
    • the other half of the live movies of Mesp1/2 gastruloids.
    • movies and dataframes classified as outlier (excluded from the analysis)

• • Note:
    • the provided movies account for about half of the movies per condition that have actually been used for the analysis presented in Figure 2 and S3. The full set of movies would have exceeded the provided storage spece on zenodo.
    • the uploaded movies are not specifically selected, they are the first 25 movies considered for the analysis.
    • the other half of the movies can be made available upon request.
      
      
      
• Figure_5_S7:
  The here provided data can replicate all graphs of Figure 5 and the corresponding supplementary Figure S7. 
  • Inlcuded:
    • all .tiff (raw) BF images from the two different analysed experiments (zipped file labeled according to the experiment name) used for the analysis from which the raw image analysis is computed.
    • an overviews folder containing figures that provide a visual overview of the imaging data and analysis per experiment and condition.
    • the PH_129_N0_50-1200_exp_combined_shape.json dataframe that contains the preprocessed data from both experiments and can be directly used to recreate all BF based graphs in Figure 5C-F and S7C-G).
    • a configs folder with the configs.yml file specified to facilitate the BF profile analysis from the PH_129_N0_50-1200_exp_combined_shape.json dataframe.
    • the elo_multi_collapse.json dataframe containing the manual annotation of elogation, multipolar, and collapsed gastruloids used in Figure 5E and S7F.
  • Not included:
    • - 
      
      
      
• Figure_6_S8,9:
  The here provided data can replicate all graphs of Figure 6 and the corresponding supplementary Figure S8 and 9. The data is separated into two parts, one containing immunofluorescent staining for the markers BRA, FOXC1, and SOX2 and one for the markers BRA, FOXC1, MEOX1, and CER1. 
  Both folders contain the following data:
  • Included:
    • the .tiff maximum projections of the individual gastruloid images from the four different analysed experiments (zipped file labeled according to the experiment name) from which the raw image analysis is computed.
    • the df_merged.json dataframe that contains the preprocessed data from all four experiments and can be directly used to recreate all graphs in Figure 6,  S8, and S9.
    • a configs folder with the configs.yml file specified to facilitate the IF profile analysis from the df_merged.json dataframe.
  • Not included:
    • the .czi raw image files from which the maximum projections are computed
    • the .tiff maxprojection files that are labeled as „outliers“ (documented in configs/config.yml file)
    • the config files for each individual experiment analysis
    • the .json data frames per condition per experiment
    • the .json data frames per experiment (merged for all conditions)
  • Note:
    • all missing config files and dataframes can be recovered by perfoming the IF_analysis from the start using the github repository linked in the corresponding publication.
    • all .czi raw image files and the .tiff maximum projections of the outliers can be made available upon request.