Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1113713 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29090800_1.fastq.gz | Fastqsanger.gz | |||
| SRR29090800_2.fastq.gz | Fastqsanger.gz | |||
| SRR29090801_1.fastq.gz | Fastqsanger.gz | |||
| SRR29090801_2.fastq.gz | Fastqsanger.gz | |||
| SRR29090802_1.fastq.gz | Fastqsanger.gz |
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Project description:Avian uterine fluid (UF) and uterovaginal sperm storage tubules (SST) are key components for acceptance of sperm in SST, sperm functions maintenance during weeks, sperm release out of SST, and their ascending through the uterus. The study of UF and SST is essential to better understand sperm storage process. The objectives were to identify proteins modulated in the hen’s oviduct by sperm, and to highlight their role during sperm storage. Two genetic lines of hens exhibiting long (F+) or short (F-) sperm storage ability were used. GeLC-MS/MS strategy was used to establish a quantitative inventory of proteins regulated after insemination in both lines. Consequently the identification of high (ANXA4/ANXA5/OCX32) and low (HSPA8/PIGR) fertility markers was investigated in uterovaginal junction by immunohistochemistry. Our results demonstrated that sperm induced a significant and rapid change in the UF proteomic content, as well as in the SST epithelium. In F+ hens, the ANXA4 protein mobilization in apical part of SST cells after insemination was associated to increased levels of some proteoglycans and binding proteins, as well as antimicrobial eggshell matrix protein (OCX32) in the UF. We also observed increased levels of lipid transporters involved in egg formation (VTG1-2, APOA1-4-H). In F- hens, insemination induced increased levels of PIGR in both UF and SST, of ANXA5 in SST, of UF enzymes exhibiting metallopeptidase activity, and mucins. In conclusion, sperm induced significant changes in the UF proteomic content. This study also provides evidence that the SST immune system is major to regulate sperm storage.
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Project description:Turkey sperm lose viability within 8-18 h when stored as liquid semen using current methods and extenders. In contrast, turkey hens maintain viable, fertile sperm in their sperm storage tubules (SST) for 45 or more days following a single insemination. Our long-term objectives are to identify and characterize differentially expressed genes that may underlie this prolonged sperm storage and then use this information to develop improved methods for storing liquid turkey semen. We employed serial analysis of gene expression (SAGE) to compare gene expression patterns in turkey SST recovered from hens after artificial insemination (AI) with extended semen (sperm AI) or extender alone (control AI). We constructed two separate SAGE libraries with SST RNA obtained from sperm and control AI hens. We used these libraries to generate 95,325 ten-base pair SAGE tags. These 95,325 tags represented 27,430 unique genes. The sperm and control AI libraries contained 47,663 and 47,662 tags representing 18,030 and 19,101 putative unique transcripts, respectively. Approximately 1% of these putative unique genes were differentially expressed (P<0.05) between treatments. Tentative annotations were ascribed to the SAGE tag nucleotide sequences by comparing them against publicly available SAGE tag and cDNA sequence databases. Based on its SAGE tag nucleotide sequence, we cloned a partial turkey avidin cDNA and confirmed its up-regulation in the sperm AI SST. The bioinformatics and experimental procedures employed to clone turkey avidin and confirm its differential expression represent a useful paradigm for analyzing SAGE tag data from relatively uncharacterized model systems. Keywords: other
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Project description:Turkey sperm lose viability within 8-18 h when stored as liquid semen using current methods and extenders. In contrast, turkey hens maintain viable, fertile sperm in their sperm storage tubules (SST) for 45 or more days following a single insemination. Our long-term objectives are to identify and characterize differentially expressed genes that may underlie this prolonged sperm storage and then use this information to develop improved methods for storing liquid turkey semen. We employed serial analysis of gene expression (SAGE) to compare gene expression patterns in turkey SST recovered from hens after artificial insemination (AI) with extended semen (sperm AI) or extender alone (control AI). We constructed two separate SAGE libraries with SST RNA obtained from sperm and control AI hens. We used these libraries to generate 95,325 ten-base pair SAGE tags. These 95,325 tags represented 27,430 unique genes. The sperm and control AI libraries contained 47,663 and 47,662 tags representing 18,030 and 19,101 putative unique transcripts, respectively. Approximately 1% of these putative unique genes were differentially expressed (P<0.05) between treatments. Tentative annotations were ascribed to the SAGE tag nucleotide sequences by comparing them against publicly available SAGE tag and cDNA sequence databases. Based on its SAGE tag nucleotide sequence, we cloned a partial turkey avidin cDNA and confirmed its up-regulation in the sperm AI SST. The bioinformatics and experimental procedures employed to clone turkey avidin and confirm its differential expression represent a useful paradigm for analyzing SAGE tag data from relatively uncharacterized model systems. Keywords: other
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Project description:Identifying smORFs and SEPs is technically and computationally challenging. Experimentally, techniques as ribosome profiling (Ribo-Seq and mass spectroscopy (MS) are used. Ribo-Seq sequences the mRNA and does not provide the translated frame, thus identifying proteins encoded by overlapping ORFs is not feasible. Herein we have used MS to characterize smORFomes of different Mycoplasma species and Escherichia coli. This data is used to corroborate the predictions of a random forest classifier that in silico predicts all the putative SEPs encoded by different bacterial genomes.
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