Ontology highlight
ABSTRACT:
PROVIDER: PRJNA791524 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17303231.fastq.gz | Fastqsanger.gz | |||
| SRR17303231_1.fastq.gz | Fastqsanger.gz | |||
| SRR17303231_2.fastq.gz | Fastqsanger.gz | |||
| SRR17303232_1.fastq.gz | Fastqsanger.gz | |||
| SRR17303232_2.fastq.gz | Fastqsanger.gz |
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Project description:The reads of duck transcripome was mapped to the duck genome and help to identify the UTR regions of predicted genes. The expression level difference between the tissue spleen and liver will help us to detect the immune-related and fatty acid metabolism related genes. Duck transcriptome was sequenced to improve the gene annotation quality, and to detect the differently expressed genes in liver and spleen tissues.
2013-04-01 | E-GEOD-22967 | biostudies-arrayexpress
Project description:The reads of duck transcripome was mapped to the duck genome and help to identify the UTR regions of predicted genes. The expression level difference between the tissue spleen and liver will help us to detect the immune-related and fatty acid metabolism related genes.
2013-04-01 | GSE22967 | GEO
Project description:Our aim was to classify and quantify transcripts identified in 24-h-cultured primary duck hepatocytes and construct a protein–protein interaction network to serve as a reference for host factors associated with hepadnavirus infection. Methods: The transcriptome of 24h-cultured PDHs was analyzed by the pair-end sequencing on the Illumina Solexa platform. High-quality reads were mapped to the Anas platyrhynchos genome with TopHat v2.0.12 software. TopHat allows multiple alignments per read and default parameters were used. Cufflinks v2.2.1 software was later used for analyses that included transcript assembly and FPKM value calculations to quantify gene expression; this program was also run with default parameters. Results: A total of 87.8 million high-quality reads were obtained from three primary duck hepatocyte samples isolated from three separate 1-day-old Anas domesticus ducklings. The reads (mean length 92.21 bases) were mapped to the Anas platyrhynchos genome. A total of 13,541 genes with > 1 fragments per kilobase of transcript per million mapped reads values were expressed in the 24-h-cultured primary duck hepatocyte samples.Using gene ontology analysis, expressed genes were assigned to functional categories. A total of 182 genes expressed in all three separate primary duck hepatocyte samples were identified as liver-specific genes. Conclusions: Transcriptome and gene ontology analyses of 24-h-cultured primary duck hepatocytes indicate that these cells retain hepatocyte-specific biological characteristics and can be used as a model system for hepadnavirus infection. A novel protein–protein interaction network suggests that host factors regulating or inhibiting innate immunity are directly associated with hepadnavirus. The transcriptome of 24h-cultured PDHs was analyzed by the paired-end sequencing on the Illumina Solexa platform.
2015-03-12 | E-GEOD-66786 | biostudies-arrayexpress
Project description:Duck reovirus (DRV), a member of the genus Orthoreovirus in the family Reoviridae, was first isolated from Muscovy ducks. The disease associated with DRV causes great economic losses to the duck industry. However, the responses of duck (Cairna moschata) to the classical/novel DRV (C/NDRV) infections are largely unknown. To reveal the relationship of pathogenesis and immune response, the proteomes of duck spleen cells under the control and C/NDRV infections were compared. In total, 5986 proteins were identified, of which 5389 proteins were quantified. The different expressed proteins (DEPs) under the C/NDRV infections showed displayed various biological functions and diverse subcellular localizations. The proteins related to the serine protease system were siginificantly changed, suggesting that the activated serine protease system may play an important role under the C/NDRV infections. Furthermore, the differences in the responses to the C/NRDV infections between the duck liver and spleen cells were compared. Only a small number of common DEPs were identified in both liver and spleen cells, suggesting diversified pattern involved in the responses to the C/NRDV infections. However, the changes in the proteins involved in the serine protease systems were similar in both liver and spleen cells. Our data may give a comprehensive resource for investigating the responses to C/NDRV infections in ducks.
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Project description:The aim of this project is to investigate the effect of stocking density on duck liver proteome.
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Project description:Our aim was to classify and quantify transcripts identified in 24-h-cultured primary duck hepatocytes and construct a protein–protein interaction network to serve as a reference for host factors associated with hepadnavirus infection. Methods: The transcriptome of 24h-cultured PDHs was analyzed by the pair-end sequencing on the Illumina Solexa platform. High-quality reads were mapped to the Anas platyrhynchos genome with TopHat v2.0.12 software. TopHat allows multiple alignments per read and default parameters were used. Cufflinks v2.2.1 software was later used for analyses that included transcript assembly and FPKM value calculations to quantify gene expression; this program was also run with default parameters. Results: A total of 87.8 million high-quality reads were obtained from three primary duck hepatocyte samples isolated from three separate 1-day-old Anas domesticus ducklings. The reads (mean length 92.21 bases) were mapped to the Anas platyrhynchos genome. A total of 13,541 genes with > 1 fragments per kilobase of transcript per million mapped reads values were expressed in the 24-h-cultured primary duck hepatocyte samples.Using gene ontology analysis, expressed genes were assigned to functional categories. A total of 182 genes expressed in all three separate primary duck hepatocyte samples were identified as liver-specific genes. Conclusions: Transcriptome and gene ontology analyses of 24-h-cultured primary duck hepatocytes indicate that these cells retain hepatocyte-specific biological characteristics and can be used as a model system for hepadnavirus infection. A novel protein–protein interaction network suggests that host factors regulating or inhibiting innate immunity are directly associated with hepadnavirus.
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