Rat_Corneal_Endothelial_Cells_EndMT_Single-Cell_RNA_Seq
Description
single-cell RNA sequencing (scRNA-seq) in a rat corneal endothelial injury and endothelial-to-mesenchymal transition (EndMT) model, linked Spp1 upregulation to EndMT. We try to establish a connection between SPP1 upregulation and guttae formation, to find a potential biomarker and therapeutic target for FECD.
Files
Steps to reproduce
scRNA-seq was performed on pooled corneal endothelium samples (n=10 rats per pool) at CON, D5, and D10. Scanpy v1.8.1 was used for Quality Control (QC) and downstream analyses. Cells with <200 detected genes, cells in the top 2% for gene/UMI counts, and cells with mitochondrial reads >20% were excluded; genes detected in <5 cells were removed. Data were library-size normalized and log-transformed; the top 2,000 highly variable genes were used for PCA (top 23 PCs), followed by Louvain clustering (resolution = 1.2) and UMAP visualization. Batch effects across time points and libraries were corrected using Harmony (v1.0) on the top PCs. After QC, a total of 49,857 high-quality cells were obtained for downstream analysis.
Institutions
- Army Medical UniversityChongqing, Chongqing