Analysis of the small non-coding RNA content of bovine oviductal extracellular vesicles during the estrous cycle
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ABSTRACT:
PROVIDER: PRJNA433714 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6704940.fastq.gz | Fastqsanger.gz | |||
| SRR6704950.fastq.gz | Fastqsanger.gz | |||
| SRR6704941.fastq.gz | Fastqsanger.gz | |||
| SRR6704951.fastq.gz | Fastqsanger.gz | |||
| SRR6704942.fastq.gz | Fastqsanger.gz |
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Project description:The success of the early reproductive events depends on an appropriate communication between gametes/embryos and the oviduct. Extracellular vesicles (EVs) contained in oviductal secretions have been suggested as new players in mediating this crucial cross-talk by transferring their cargo (e.g. proteins, mRNA and small ncRNA) from cell to cell. However, little is known about the oviduct EVs composition and their implications in reproductive success. The objective of our study was to determine the changes of oviductal EVs mRNA content under the hormonal influence during the estrous cycle. Methods: EVs, exosomes and microvesicles, were isolated from bovine oviductal fluid at different stages of the estrous cycle (postovulatory-stage, early luteal phase, late luteal phase and pre-ovulatory stage). Total RNA was isolated and used for the preparation of RNA-seq libraries. RNA-sequencing was performed on an Illumina HiSeq 2500. The obtained sequence reads that passed quality filters were mapped to the bovine genome sequence using Hisat 2. Read counts were calculated with QuasR Qcount and statistical analysis with EdgeR to identify differential mRNA abundance across the different stages of the estrous cycle. Results: RNA-sequencing identified 903 differentially expressed transcripts (FDR<0.001) in bovine oviductal EVs across the estrous cycle. Major differences were found between post-ovulatory and the rest of the stages analyzed.Functional annotation of the differentially abundant mRNAs identified functions related to cilia expression, exosome/vesicles, and many transcripts encoding ribosomal proteins. Conclusions: Our findings represent the first extensive oviductal signature of bovine oviductal EVs mRNA content and contribute to a better understanding of the role of EVs as modulators of gamete/embryo-maternal interactions.
2018-07-31 | GSE110399 | GEO
Project description:The success of the early reproductive events depends on an appropriate communication between gametes/embryos and the oviduct. Extracellular vesicles (EVs) contained in oviductal secretions have been suggested as new players in mediating this crucial cross-talk by transferring their cargo (e.g. proteins, mRNA and small ncRNA) from cell to cell. However, little is known about the oviduct EVs composition and their implications in reproductive success. The objective of our study was to determine the changes of oviductal EVs small ncRNA content under the hormonal influence during the estrous cycle. Methods: EVs, exosomes and microvesicles, were isolated from bovine oviductal fluid at different stages of the estrous cycle (postovulatory-stage, early luteal phase, late luteal phase and pre-ovulatory stage). RNA enriched for short molecules was isolated and used for the preparation of small RNA-seq libraries. RNA-sequencing was performed on an Illumina HiSeq 2500. The obtained sequence reads that passed quality filters were annotated by BLAST alignment to various sets of non-coding and coding RNAs. Read counts were calculated based on the frequency of unique sequences after removal of PCR duplicates. Statistical analysis was done with EdgeR to identify differential small ncRNA abundance across the different stages of the estrous cycle. Results: Small RNA-Seq identified the presence of different types of ncRNAs (miRNAs, rRNA fragments, tRNA fragments, snRNA, snoRNA, and other ncRNAs), which were partially also under hormonal influence. Major differences were found between post-ovulatory and early luteal and the rest of the stages for small ncRNAs. Interesting miRNAs identified in oviductal EVs, miR-34b and miR-449a, showed differential abundance among stages. Dysregulation of these miRNAs has been associated with defective cilia in the oviduct and infertility. Conclusions: Our findings represent the first extensive oviductal signature of bovine oviductal EVs miRNA content and contribute to a better understanding of the role of EVs as modulators of gamete/embryo-maternal interactions.
2018-07-31 | GSE110443 | GEO
Project description:Analysis of the mRNA content of bovine oviductal extracellular vesicles during the estrous cycle
| PRJNA433626 | ENA
Project description:Analysis of the mRNA and small non-coding RNA content of bovine oviductal extracellular vesicles during the estrous cycle
| PRJNA433697 | ENA
Project description:The success of the early reproductive events depends on an appropriate communication between gametes/embryos and the oviduct. Extracellular vesicles (EVs) contained in oviductal secretions have been suggested as new players in mediating this crucial cross-talk by transferring their cargo (e.g. proteins, mRNA and small ncRNA) from cell to cell. Therefore, the objective of the project was to analyze the protein content of EVs (exosomes and microvesicles) contained in the bovine oviductal fluid at different stages of the estrus cycle. For this purpose, pairs of oviducts with their attached ovaries were collected from cyclic cows at a local abattoir under different hormonal regulation along the estrous cycle. Oviducts were classified into one of the 4 stages of the estrous cycle according to the morphology of the corpus lutea(CL) and follicle populations: Stage 1 (S1): showed recently ovulated follicle (d 1 to 4 of estrous cycle); Stage 2 (S2): early luteal development with medium or large or both present (d 5 to 11); Stage 3 (S3): fully functional CL yellow or orange in color (d 11 to 17); or Stage 4 (S4): regressing CL with little vasculature and a large preovulatory follicle present (d 18 to 20). EVs were collected by ultracentrifugation and prepared for mass spectrometry analysis.
2018-07-31 | PXD008851 | Pride
Project description:comparison miRNA content between extracellular vesicles from AAV-transduced or intact cells
2021-08-07 | E-MTAB-10858 | biostudies-arrayexpress
Project description:Purpose: Extracellular vesicles (EVs) are nanoparticles that can be secreted by different cells, including cells found within the ovarian follicle. Currently, EVs are considered an important form of intercellular communication, since they carry biological contents. The goal of this study was to survey the effects of small EVs from follicles at different estrous cycle stage in bovine cumulus cells. Methods: We used an established model to obtain follicular fluid (FF) at early and late estrous cycle stage according to corpus luteum appearance, corresponding to low and high progesterone (P4) levels, respectively. We collected FF from 3-6 mm follicles and isolated small EVs, which were used as a supplement during in vitro maturation (IVM). Cumulus cells were collected from cumulus-oocyte complexes (COCs) pools and the RNAs were obtained and subjected to RNA sequencing. Results: The results showed that small EVs from different estrous cycle stage are capable to affect transcripts in cumulus cells and modulate different pathways and biological processes related to oocyte maturation, ovulation and immune response. Conclusion: This study demonstrated that small EVs from low and high P4 group impact the RNA profile in cumulus cells after 9 hours of in vitro maturation.
2019-12-02 | GSE133587 | GEO
Project description:This study attempted to reveal the profile of the oviductal gene expression at each stage of estrous cycle by microarray analyses The oviductal tissue was separately collected at four stages of the estrous cycle, i.e., proestrus, estrus, metestrus, and diestrus.
2012-01-01 | E-GEOD-25875 | biostudies-arrayexpress
Project description:Objective To investigate the influence that oviductal extracellular vesicles from patients with endometriosis exert on early embryo development. Design In vitro experimental study Setting University-affiliated hospital. Patient(s) Women with and without endometriosis who underwent hysterectomy (n = 15 in total). Intervention(s) None. Main Outcome Measure(s) Oviductal extracellular vesicles from patients with endometriosis (oEV-EMT) or without endometriosis (oEV-ctrl) were isolated and co-cultured with two-cell murine embryos for 75 hours. Blastocyst rates were recorded. RNA sequencing was used to identified the differentially expressed genes in blastocysts cultured either with oEV-EMT or with oEV-ctrl. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed to identify potential biological processes in embryos that oEV-EMT affect. The functions of oEV on early embryo development were determined by reactive oxygen species (ROS) levels, mitochondrial membrane potentials, total cell numbers and apoptotic cell proportions. Result(s) Extracellular vesicles were successfully isolated from human Fallopian tubal fluid and their characterizations were described. The blastocyst rates were significantly decreased in the oEV-EMT group. RNA sequencing revealed that oxidative phosphorylation was down-regulated in blastocysts cultured with oEV-EMT. Analysis of oxidative stress and apoptosis at the blastocysts stage showed that embryos cultured with oEV-EMT had increased ROS level, decreased mitochondrial membrane potentials, and increased apoptotic index. Total cell numbers were not influenced. Conclusion(s) Oviductal extracellular vesicles from patients with endometriosis exert a negative influence on early embryo development.
2023-06-02 | GSE225323 | GEO
Project description:This study attempted to reveal the profile of the oviductal gene expression at each stage of estrous cycle by microarray analyses
2012-01-01 | GSE25875 | GEO