Spatiotemporal Dynamics of Skin Wound Healing

This repository contains the data processing and analysis scripts for our single-cell RNA-seq and Spatial transcript (ST-seq) of skin wound healing study leaded by Liu et al..

Liu, Z., Li, D., Bian, X., Luo, L., Björklund, Å.K., Li, L., Zhang, L., Chen, Y., Guo, L., Gao, J., et al. (2024). Spatiotemporal Single-Cell Roadmap of Human Skin Wound Healing. bioRxiv, 2024.2008.2030.609923. 10.1101/2024.08.30.609923

https://www.biorxiv.org/content/10.1101/2024.08.30.609923v1

Repository Contents

• 01-scRNAseq Acute Wounds contains scripts and notebooks used for running CellRanger, Removing Doublets, Seurat, cell-cell crosstalk analysis, subclustering analysis of acute wounds, and Milo cell abundance analysis.
• 02-STseq Acute Wounds contains scripts used for running SpaceRanger, standard seurat analysis and plotting, and preparation for deconvolution.
• 03-Deconvolution contains scripts and notebooks used for running the deconvolution analysis of spatial data and bulk RNA-seq data based on the cell type signatures in scRNA-seq.
• 04-Data Integration contains scripts and notebooks used for integrating scRNA-seq datasets from different sources. e.g. healthy adult skin scRNA-seq, diabetic foot ulcer scRNA-seq, venous ulcer scRNA-seq, and acute wound scRNA-seq.
• 05-Cross species analysis contains scripts used for corss-species comparison of human and mouse wound healing.
• EGA submission contains scripts used for EGA data submission.
• Rshiny scwoundatlas contains scripts used for creating RShiny visualization tool in our website.
• custom functions contains scripts used for common functions.
• scripts reproduce figures contains scripts used for reproducing figures in our manuscript.
• scripts paper revision contains scripts used for first revision.
• webatlas_vistool contains pipelines running for WebAtlas spatial visualization tool.

Data Available

Web portal (Rshiny and WebAtlas tool)

Processed data can be accessed on our web portal at https://www.xulandenlab.com/tools

Raw sequencing data

Original data sequenced in this study have been deposited in gene expression omnibus (GEO) under assession numbers: GSE241132, GSE265972, GSE241124, and GSE218430.

Contact and collaboration

Feel free to post an issue in this repository or contact by email zhuang.liu[at]ki.se or ning.xu[at]ki.se if you have any questions.