zebTestis

Codes for the projects of zebrafish testis scRNA-seq analysis. Inlcuding cell ranger preprocess, seurat analysis, GO enrichment analysis, and ligand-receptor analysis.

fastq2matrix

Convert fastq files into UMI matrix through running cell ranger.

basicAnalysis

Analyses including Seurat cell cluster analysis, marker gene finding, and ClusterProfiler GO enrichment analysis.

LRanalysis

Ligand-receptor analysis for paracrine cell-cell communcation.

Data availability

raw sequencing data

cellranger matrix files

Seurat rds file with cell annotation and UMAP

Citation:

Qian P, Kang J, Liu D and Xie G (2022) Single Cell Transcriptome Sequencing of Zebrafish Testis Revealed Novel Spermatogenesis Marker Genes and Stronger Leydig-Germ Cell Paracrine Interactions. Front. Genet. 13:851719. doi: 10.3389/fgene.2022.851719