Ontology highlight
ABSTRACT:
PROVIDER: PRJEB44919 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| cohort188.ALL.1-28.vcf.gz | Vcf | |||
| cohort188.ALL.1-28.vcf.gz.tbi | Vcf |
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Project description:To characterize breed-specific difference among four Korean native chicken breeds and White Leghorn, we measured their transcriptomes at liver tissue using Affymetrix Chicken gene 1.0 ST array platform.
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Project description:The Yeonsan Ogye (Ogye) is the rare black chicken breed domesticated in Korean peninsula, which has been noted for entire black color upon its appearances including feather, skin, comb, eyes, shank, claws and internal organs. In this study, whole genome, transcriptome and epigenome sequencings of Ogye were performed using high-throughput NGS sequencing platforms. We have produced Illumina short-reads (Paired-End, Mate-Pair and FOSMID) and PacBio long-reads for whole genome sequencing (WGS), 1.4 billion reads for RNA-seq, and 123 million reads for RRBS (reduced representation bisulfite sequencing) data. Using WGS data, Ogye genome has been assembled, and coding/non-coding transcriptome maps were constructed on Ogye genome given largescale sequencing data. We have predicted 17,472 (3,550 newly annotated and 13,922 known) protein-coding transcripts, and 9,443 (6,689 novel and 2,754 known) long non-coding RNAs (lncRNAs).
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Project description:The Yeonsan Ogye (Ogye) is the rare black chicken breed domesticated in Korean peninsula, which has been noted for entire black color upon its appearances including feather, skin, comb, eyes, shank, claws and internal organs. In this study, whole genome, transcriptome and epigenome sequencings of Ogye were performed using high-throughput NGS sequencing platforms. We have produced Illumina short-reads (Paired-End, Mate-Pair and FOSMID) and PacBio long-reads for whole genome sequencing (WGS), 1.4 billion reads for RNA-seq, and 123 million reads for RRBS (reduced representation bisulfite sequencing) data. Using WGS data, Ogye genome has been assembled, and coding/non-coding transcriptome maps were constructed on Ogye genome given largescale sequencing data. We have predicted 17,472 (3,550 newly annotated and 13,922 known) protein-coding transcripts, and 9,443 (6,689 novel and 2,754 known) long non-coding RNAs (lncRNAs).
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Project description:Korean native cattle (Hanwoo) Genome sequencing
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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.
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