Ontology highlight
ABSTRACT:
PROVIDER: PRJNA795703 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17509708_1.fastq.gz | Fastqsanger.gz | |||
| SRR17509708_2.fastq.gz | Fastqsanger.gz | |||
| SRR17509709_1.fastq.gz | Fastqsanger.gz | |||
| SRR17509709_2.fastq.gz | Fastqsanger.gz | |||
| SRR17509710_1.fastq.gz | Fastqsanger.gz |
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Project description:Liver is the major organ of lipid biosynthesis in chicken. In laying hens, the liver synthesizes most of yolk precursors and transports to the developing follicles to produce eggs. However, a systematic and comprehensive investigation of long non-coding RNAs (lncRNAs) and mRNAs transcriptome in chicken liver across different developmental stages remain clearly unknown. Here, we constructed 12 RNA libraries from liver tissue during four developmental stages, including juvenile period (JP, day 60), sexual maturity period (SM, day 133), peak laying period (PL, day 220) and broodiness period (BP, day 400). A total of 16,930 putative lncRNAs and 18,260 mRNAs were identified among these samples. More than half of identified lncRNAs were intergenic lncRNAs (lincRNAs), accounting for 53.70%. The temporal expression pattern showed that lncRNAs were more restricted than mRNAs. We identified numerous differentially expressed lncRNAs (DE lncRNA) and mRNAs (DEGs) by pairwise comparisons between the four developmental stages and found that vitellogenin 2 (VTG2), riboflavin binding protein (RBP), and a novel protein-coding gene were differentially expressed in all stages. Time-series analysis showed that the module with up-regulated genes were enriched in related to lipid metabolism process. Co-expression networks suggested the functional relatedness between mRNAs and lncRNAs and the results showed the DE-lncRNAs also mainly involve in lipid biosynthesis and metabolism process. These results suggest the transcriptome variation of liver in different developmental stages and improve the comparative understandings of molecular mechanisms of liver development in chickens.
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Project description:The objective of this study was to identify candidate genes associated with sexual maturity and ovary development of chicken. Gene expression profiling sequencing analysis was employed using pre-laying (P-F-O1, L-F-O1) and laying ovaries (P-F-O2, L-F-O2) from two sub-breeds of Ningdu Yellow chicken. RNA-seq data and qPCR showed that HEP21 significantly differential expressed between the pre-pubertal ovary and pubertal ovary. A total of 23 variations were detected on HEP21. Association analysis between SNP in HEP21 and chicken reproductive traits showed that rs315156783 was significantly related to chicken comb height at 84 and 91 days.
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