Abstract
The domestic chicken (Gallus gallus domesticus) is an important model organism for both developmental biology and agricultural production. However, a comprehensive expression atlas of chickens, especially for layers, is still missing. Here, we performed RNA sequencing of 20 tissues collected from Lohmann white chickens at three developmental stages (E18, D1, W30). We built a freely available web server (http://scrna.avianscu.com/chickenatlas/) to store, visualize, and share our data. We identified a large number of tissue-specific expressed genes. Combined with single-cell RNA sequencing data of chicken embryos, we found that COL9A1, expressed in the middle of the growth plate of the tibia, may be a new marker gene for chondrocyte differentiation. Furthermore, we identified several potential master regulators for specific tissue, such as HNF4A, HNF1A, and FOXA3 for the liver, and MEF2C for the heart. In conclusion, we have built a comprehensive gene expression atlas of chickens, which will be a valuable resource to the community for both basic biological and poultry breeding research.