README.md

ZebEndoimmune

The scripts used to analyze zebrafish endothelial single-cell sequencing data

Raw sequencing data (fastq and matrix data)

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE276251

step1: run cell ranger based on fastq files

step1_rawDataAnalysis

step2: run seurat on all the cells detected

step2_preAnalysis

step3: subpopulation analysis on all endothelia cells

3.1 select the cell clusters belong to ECs (based on the EC marker genes)

cell cluster information can be found in step2_preAnalysis/extract_cell_clusters/cell_cluster_ids.tsv

The clusters 0, 1, 2 were identified as endothelial cells (EC) for further EC subpopulation studies.

3.2 further analysis on those ECs by Seurat

step3_ECSubpopulationAnalysis

citation:

Wang Xiaoning, Zhao Jinxiang, Xu Jiehuan, Li Bowen, Liu Xia, Xie Gangcai, Duan Xuchu, Liu Dong (2024) Noncaloric monosaccharides induce excessive sprouting angiogenesis in zebrafish via foxo1a-marcksl1a signal eLife 13:RP95427.https://doi.org/10.7554/eLife.95427.2