Spinal-cord-scRNAseq

This repository contains supplementary code for the analyses presented in the manuscript: Microglia coordinate intracellular interactions during spinal cord repair in mice.

If you have any questions or feedback regarding the code, please contact Cankun Wang via [email protected].

Directory structure

rmarkdown/: analysis code and the generated reports

1. 1_load_and_integration: Data load and library integration (For Fig. 5 and Sup. Fig. 8)
2. 2_microglia_analysis: Microglia cluster analysis (For Fig. 5 and Sup. Fig. 8)
3. 3_mdm_analysis: MDM cluster analysis (For Fig. 6 and Sup. Fig. 9 and 10)
4. 4_astrocyte_analysis: Astrocyte cluster analysis (For Fig. 7)
5. 5_Endothelial_analysis: Endothelial cluster analysis (For Sup. Fig. 11)
6. 6_Ependymal_analysis: Ependymal cluster analysis (For Sup. Fig. 12)
7. 7_Oligodendrocyte_analysis: Oligodendrocyte lineage cluster analysis (For Sup. Fig. 13)
8. 8_Neutrophil_analysis: Neutrophil cluster analysis (For Sup. Fig. 14)
9. 9_Monocyte_analysis: Monocyte cluster analysis (For Sup. Fig. 15)
10. 10_cellchat: CellChat analysis
11. monocle_f.R: Pseudotime analysis on Microglia and MDM cells

NOTE:

• You may find a data folder shown in the code. This folder contains processed R object and results. The repository does not provide data/ folder since it is too large (1.2GB). Please download from here: https://zenodo.org/records/6590561.
• The volcano plots were generated by copying data from the exported DEG CSV files using graphpad prism.

Code authors

• Faith Brennan
• Yang Li
• Qi Guo
• Cankun Wang