scRNAseq and BulkRNAseq scripts for "Structured wound angiogenesis instructs mesenchymal barrier compartments in the regenerating nerve" publication. DOI:https://doi.org/10.1016/j.neuron.2023.10.025
Code Authors: Aurora Maurizio, Stefano de Pretis, Santo Diprima
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- Tomato_scRNAseq_full_ds.R [TdTomato scRNAseq full dataset (containing also MES, pericytes, and LEC) prepropressing.]
- Tomato_scRNAseq_EC_only_ds.R [Analysis and carachterization of EC only clusters, isolated from the TdTomato scRNAseq full dataset]
- Pdgfrb_scRNAseq_ds.Rmd [Analysis and carachterization of Pdgfrb MES cells]
- Carr_reanalysis.R [Re-analysis of Carr et al. 2019 scRNAseq dataset. GSE120678]
- Toma_reanalysis.R [Re-analysis of Toma et al. 2020 dataset. GSE147285]
- Kalinski_reanalysis.R [Re-analysis of Kalinski et al. 2020 dataset. GSE153762]
- Toma_Carr_Kalinski_Bonanomi_alluvial.R [Alluvial plot of the relative abundance of EC subtypes in the intact nerve or at different days post injury.]
- Milich_EC_label_transfer_alluvial.R [Re-analysis of Milich et al. 2021 spinal cord injury dataset. GSE162610]
- Ydens_reanalysis.R [Re-analyisis of Ydens et al. 2020 dataset. GSE144708]
- Merge_EC_MACs_SCHW_MES_Carr.R [Cells from different tissues and datasets were merged and clustered]
- CellChat_EC_MACs_SCHW_MES_Carr.R [Cell-Cell communication analysis with CellChat. EC, FIBRO Carr et al. 2019, MACS, SCHWANN]
- CellChat_MES.R [interaction pairs heatmap (Suppl Fig 5 U and V)]
- CellChat_MES_Pdgfrb.Rmd [Cell-Cell communication analysis with CellChat. EC, Pdgfrb FIBRO, MACS, SCHWANN]
- Kalucka_reanalysis.R [Re-analysis of Kalucka et al. 2020 dataset. GSE99235]
- monocle_pseudotime.R [EC pseudotime analysis with monocle2]
- velocity_Injury.ipynb [7DPI EC RNA velocity analysis with scVelo]
- velocity_Uninjured.ipynb [Intact EC RNA velocity analysis with scVelo]
- Pdgfrb_velocity_Injury.ipynb [Intact, 7DPI, 21DPI Pdgfrb MES RNA velocity analysis with scVelo]
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- bulkRNASeq_Cherry.R [DGE analysis of our 7DPI WT and KO Cherry EC samples]
- bulkRNASeq_Tomato.R [DGE analysis of our intact, 7 DPI, 14 DPI TdTomato EC samples]
- metadata_cherry_tomato.xlsx [sample metadatda for our Cherry and TdTomato EC samples ]
- bulkRNASeq_Tomato_Corada.R [DGE analysis of our intact, 7 DPI, 14 DPI TdTomato samples + Corada et al. 2019 embryo and Adult samples. GSE122564 ]
- metadata_tomato_corada.xlsx [sample metadatda for our TdTomato samples and Corada et al. 2019 samples. GSE122564]
- EWCE.R [Expression Weighted Cell Type Enrichment analysis to check the distribution of DEGs among EC subtypes]
- Associate_celltype_with_gene_name.R [DEG gene annotation according to scRNAseq expression]