Transcriptome Profiling of Hypothalamus and Ovary Reveals Key Regulators of Egg Production in Inner Mongolia Bian Chicken vs. Grassland Green Bird Chicken

This dataset contains the raw and processed transcriptome sequencing data (RNA-seq) comparing the hypothalamus and ovary tissues between two chicken breeds: the indigenous Inner Mongolia Bian chicken (BH/BO) and the high-yielding Grassland Green Bird chicken (CH/CO). Study Overview: To identify key genetic regulators of egg production performance, we performed RNA-seq on hypothalamus and ovary tissues from 4 Bian chickens and 3 Green Bird chickens at 33 weeks of age (peak laying period). Key Findings: 1. Differential Expression: - Hypothalamus: 177 differentially expressed genes (DEGs) identified (106 up-regulated, 71 down-regulated). - Ovary: 503 DEGs identified (137 up-regulated, 366 down-regulated). 2. Functional Enrichment: - GO Analysis: DEGs were significantly enriched in calcium ion binding, RNA polymerase II transcription regulation, hormone binding, and defense responses. - KEGG Pathways: Significant enrichment in PI3K-Akt signaling, Neuroactive ligand-receptor interaction, Calcium signaling, AMPK signaling, and cAMP signaling pathways. 3. Key Candidate Gene: - We identified LOC107050261 (Peroxisomal biogenesis factor 19-like) as a significantly down-regulated gene in Bian chicken hypothalamus. - GO enrichment suggests its involvement in lipid binding regulation, suggesting a potential role in steroid hormone synthesis and follicle development, making it a key candidate gene for regulating egg production traits in Bian chickens. Data Files Included: - diff_expression_hypothalamus.xlsx : DEG list for Hypothalamus (BH vs CH) - diff_expression_ovary.xlsx : DEG list for Ovary (BO vs CO) - heatmap_hypothalamus.pdf : Hierarchical clustering heatmap of DEGs in Hypothalamus - heatmap_ovary.pdf : Hierarchical clustering heatmap of DEGs in Ovary - volcano_hypothalamus.png : Volcano plot for Hypothalamus DEGs - volcano_ovary.png : Volcano plot for Ovary DEGs - kegg_pathway_analysis.xlsx : Detailed KEGG enrichment results - go_enrichment_analysis.xlsx : Detailed GO enrichment results - README.txt : Detailed file descriptions, methods, and contact information Note: Raw sequencing reads (.fastq.gz) are available upon reasonable request due to file size limitations. All downstream analyses were performed using standard pipelines (HISAT2, StringTie, DESeq2, clusterProfiler). License: CC-BY 4.0 Contact: [e-mail] Affiliation: Inner Mongolia Agricultural University