This repository includes data and codes associated with the manuscript Thowfeequ, Fiorentino et al, Characterisation of the transcriptional dynamics underpinning the function, fate, and migration of the mouse Anterior Visceral Endoderm, bioRxiv, 2021. We provide three Jupyter notebooks for the analysis of a Visceral Endoderm enriched single-cell RNA-sequencing dataset of mouse embryos at the stages E5.5 and E6.25, obtained through the Smart-seq2 protocol.
The SoS Polyglot notebooks "E55_Analysis.ipynb" and "E625_Analysis.ipynb" include the following analyses at the stages E5.5 and E6.25, respectively:
- Highly Variable Genes identification
- Iterative cell clustering
- Computation of marker genes for each cluster
- Diffusion pseudotime analysis for Anterior Visceral Endoderm (AVE) and emVE cells
The python3 Jupyter notebook "RNA_velo_Analysis.ipynb" includes the RNA velocity analysis on AVE and emVE cells, performed with the scvelo implementation, at the stages E5.5 and E6.25, both separated and integrated.