Functional Annotation of Chicken Genome

The identification of regulatory elements is a key step in understanding how an organism’s genotype determines the phenotype. The ENCODE projects have made significant progress in this area for human and mouse, and the FAANG project aims to utilize information learned from ENCODE and leverage technology and assays available for the FAANG project to functionally annotate farm animals including chickens. Other than the major chicken tissues, additional tissues were collected from: bone marrow, heart, kidney, shellgland, testis, thymus, trachea and F1 Follicle. To ensure data integrity, two biological replicates will be used to validate consistency. Seven libraries will be prepared per tissue sample: RNA-seq, ATAC-seq, and four ChIP-seq (H3K4me3, H3K27me3, H3K4me1, H3K27ac, input). To integrate all the data and generate comprehensive functional annotations, ChromHMM will be used.