Project description:We report the transcriptomes of 10 different chicken (Gallus gallus) cell/tissue types. The goal of this project was to determine similarities and differences between different cell/tissue types, with respect to protein coding genes, lncRNA, isoform counts, and differential gene expression. We provide raw data and bigWig files for UCSC visualization. The findings described here will be useful towards a complete annotation of chicken tissue and cellular transcriptomes.
Project description:The Yeonsan Ogye, a culturally significant but small Korean chicken breed has been extensively studied for its fibromelanosis, leaving its low body weight and growth rate relatively unexplored. Here we present the first comparative hepatic transcriptome analysis of Ogye and the heavy, fast-growing Korean Brown Cornish breed at the critical stages of 5 and 10 weeks of age. Using RNA sequencing (RNA-seq) and bioinformatic analyses we uncovered significant and dynamic differences between the breeds. At 5 weeks, Ogye livers exhibited enriched inflammatory and energy-transfer processes (oxidoreductase activity, mitochondrial function), whereas in Cornish livers, translational and macromolecule biosynthesis pathways (ribosomal structure, RNA binding) were enriched. By 10 weeks, Ogye shifts further toward immune- and stimulus-response functions (cytokine/chemokine signaling, MAPK pathway, oxidative phosphorylation), while Cornish maintains elevated protein modification, intracellular transport, and RNA processing activities. Moreover, within the differentially expressed MAPK signaling pathway, genes involved in the regulation of cellular metabolism (FGF19, DUSP8, PTPRR, CACNA1C, CACNA1S, among others) were upregulated in Ogye while growth factor-related genes (IGF1, IGF2, EGFR, VEGFC, and FGFR3) stood out among the Cornish chicken. These patterns suggest contrasting metabolic signatures — a high maintenance, energy expending profile in Ogye versus a growth efficient, anabolic profile in Cornish — and reveal temporal switching of core pathways across development. Consequently, our findings provide a basis for future initiatives aimed at developing biotechnological solutions to enhance growth and weight gain in Ogye and potentially other small chicken breeds.
Project description:Expression of known and predicted genes in tissues of Gallus gallus (chicken) pooled from multiple healthy individuals. Two-colour experiments with two different tissues hybridized to each array. Each tissue is arrayed in replicate with dye swaps. Tissues: Bursa of Fabricius, Cerebellum, Cerebral cortex, Eye, Femur with bone marrow, Gallbladder, Gizzard, Heart, Intestine, Kidney, Liver, Lung, Muscle, Ovary, Oviduct, Skin, Spleen, Stomach, Testis, Thymus
Project description:RNA samples from chicken (Gallus gallus) embryonic fibroblasts (sample ID: ES90) as well as from the HD11 chicken macrophage cell line (sample ID: ES91) were sequenced at the National Institutes of Health Intramural Sequencing Center (NISC) using the Illumina GAIIx technology running the standard CASAVA/ELAND pipeline.
