As part of the Farm animal Genotype-Tissue Expression (FarmGTEx) project, we describe a comprehensive reference map comprising 1,793,854 cells from 59 cattle tissues, spanning both sexes and multiple developmental stages. This map, generated by single-cell/nucleus RNA sequencing, identifies 131 distinct cell types, revealing intra- and inter-tissue cellular heterogeneity in gene expression, transcription factor regulation, and intercellular communication. Integrative analysis with genetic variants that underpin various bovine monogenic and complex traits uncovers cell types of relevance, such as spermatocytes responsible for sperm motilities and excitatory neurons for milk fat yield. Comparative analysis reveals similarities in gene expression between cattle and humans at single-cell resolution, allowing for detection of relevant cell types for studying human complex phenotypes. This cattle cell atlas will serve as a key resource for cattle genetics and genomics, immunology, comparative biology, and ultimately human biomedicine.
⚫Raw sequencing data processing, quality control and cell clustering
⚫Cell cycle analysis
⚫Cell communication analysis
⚫Gene regulatory network analysis
⚫Pseudo time trajectory analysis
⚫Cell type preference analysis
⚫Sex bias analysis
⚫High-dimensional weighted gene co-expression network analysis
⚫Gene function enrichment analysis
⚫Enrichment analysis between cell types and monogenic disorders
⚫Enrichment analysis between cell types and complex traits
⚫Linkage disequilibrium score regression analysis
Cattle Cell Atlas: a multi-tissue single cell expression repository for advanced bovine genomics and comparative biology (Preprint)
Bo Han,#, Houcheng Li,#, Qi Zhang,#, Weijie Zheng1,#, Ao Chen,#, Senlin Zhu,#, Tao Shi,#, Yali Hou,#, Fei Wang,#, Dong Zou, Zhixiang Yuan, Yu Song, Wen Ye, Aixia Du, Yihan Fu, Minghui Jia, Zhonghao Bai, Wansheng Liu, Wenbin Tuo, Jayne C. Hope, David E. MacHugh, John Francis O’ Grady, Ole Madsen, Goutam Sahana, Yonglun Luo, Lin Lin, Congjun Li, Zexi Cai, Lin Liu, Zhang Zhang, Zhu Ma, George E. Liu*, Huizeng Sun*, Yu Jiang*, Lingzhao Fang*, Dongxiao Sun*