Expression of lncRNA and mRNA in the cumulus-oocyte complex of rabbits exposed to ammonia
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ABSTRACT:
PROVIDER: PRJNA1190847 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31513200_1.fastq.gz | Fastqsanger.gz | |||
| SRR31513200_2.fastq.gz | Fastqsanger.gz | |||
| SRR31513198_1.fastq.gz | Fastqsanger.gz | |||
| SRR31513198_2.fastq.gz | Fastqsanger.gz | |||
| SRR31513199_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Background: Ammonia (NH3) is an environmental pollutant and a potent reproductive stressor widely found in rabbit houses. Exposure to ammonia can result in follicle atresia, affect oocyte maturation and cause cumulus cell apoptosis. Long non-coding RNA (lncRNA) is an important factor in the regulation of cumulus cell development and oocyte maturation. The potential molecular mechanism of NH3 in the induction of cumulus-oocyte complex (COCs) toxicity and the regulatory role of lncRNA in COCs are currently unclear. Methods: A total of 150 female IRA rabbits (35 days old) were randomly divided into three groups, and kept in environmental control rooms for four weeks. The rabbits in the control group (CG) were kept under an NH3 concentration of < 3 ppm. The two treatment groups were kept under NH3 concentrations of 10 ppm (low ammonia concentration, LAC) and 30 ppm (high ammonia concentration, HAC). We used a combination of RNA deep sequencing, quantitative real-time polymerase chain reaction (qRT-PCR), and bioinformatic analysis to explore the regulatory mechanism of lncRNA and messenger RNA (mRNA) in COCs. Results: The results from Gene Ontology (GO) items showed that female meiosis sister chromatid cohesion and the regulation of follicle-stimulating hormone secretion were involved in the mechanism of rabbits exposed to NH3. The results demonstrated that the mammalian target of the rapamycin (mTOR) signaling pathway and the transforming growth factor-beta (TGF-beta) signaling pathway inhibits germ cell development and follicular growth in the LAC versus the CG group. LncRNAs were involved in the apoptosis of female germ cells via the hypoxia-inducible factor (HIF-1) signaling pathway in the HAC versus the CG group. Co-expression analysis found that lncRNA MAPK3 and lncRNA SHC1 were correlated with changes in cumulus cell and oocyte function after NH3 exposure. Conclusions: These results indicate that NH3 affected the development and function of COCs by influencing lncRNA expression.
2025-06-16 | GSE282848 | GEO
Project description:The palmitoyl-proteome of bovine cumulus-oocyte complexes (COCs) cells was investigated by combining acyl-biotin exchange chemistry and quantitative mass spectrometry analysis.
2022-02-15 | PXD020540 | Pride
Project description:The oocyte forms a complex with their somatic cumulus cells within the follicle throughout the preovulatory maturation steps. Cumulus cells support their oocyte not only through mechanical protection but also with a close bidirectional exchange of metabolites. Analysis of the oocytes cumulus gives the opportunity to explore non-invasively oocytal well-being and quality. In vitro maturation (IVM) is the first rate-limiting step in in vitro embryo production. Analysis of protein expression in cumulus cells around this critical step helps to explore the impact of maturation conditions and to examine an influence on maturational competence of the oocyte. The goal of this study was the comparison of the cumulus proteome of oocytes with and without maturational competence matured under in vivo and in vitro conditions. Therefore twenty cumulus samples corresponding to single oocytes were analysed. Half of the samples were matured in vivo and the other half in vitro. For each maturation group, cumulus from oocytes matured successfully (SM; n=5) and failed to mature (FM; n=5) were analysed.
2020-06-30 | PXD016679 | Pride
Project description:Cytoplasmic and nuclear maturation of oocytes as well as interaction with the surrounding cumulus cells are important features relevant to the acquisition of developmental competence. We used brilliant cresyl blue (BCB) to distinguish oocytes with low activity of the enzyme Glucose-6-Phosphate Dehydrogenase, and thus separated fully grown (BCB+) oocytes from those in the growing phase (BCB-). The BCB+ oocytes are twice as likely to produce a blastocyst in vitro compared to BCB- oocytes (P<0.01). We analyzed mitochondrial DNA (mtDNA) copy number in single oocytes and determined that BCB- oocytes have 1.3-fold more copies than BCB+ oocytes (P=0.004). We also interrogated the transcriptome of oocytes and surrounding cumulus cells of BCB+ versus BCB- oocytes. There was no differential transcript abundance of genes expressed in oocytes, but we identified 172 genes in cumulus cells with differential transcript abundance (FDR<0.05) based on the BCB staining of their oocyte. Differential gene co-expression analysis between BCB+ and BCB- oocytes and their surrounding cumulus cells revealed dynamic coordination of transcript abundance between both compartments of the cumulus-oocyte complex. We identified a subset of genes whose co-expression in fully grown oocytes (n=75) and their surrounding cumulus cells (n=108) compose a unique profile of the cumulus-oocyte complex. In conclusion, as oocytes transition from growing to fully grown, there is an increase in the likelihood of producing a blastocyst, a reduction of mtDNA copies and no systematic variation of transcript abundance. Cumulus cells present changes in transcript abundance, which reflects in a dynamic co-expression between oocyte and cumulus cells.
2022-03-28 | GSE199210 | GEO
Project description:Transcriptomes of mouse mural granulosa cells were sequenced to identify transcripts expressed in mural granulosa cells of ovaries. Moreover, transcriptomes of cumulus cells were compared between those of young (2 month-old) and old mice (10 month-old) to assess the effects of ageing on cumulus cells. In addition, transcriptomes of cumulus-oocyte complexes were compared between DBA/2 and (C57BL/6 x DBA/2)F1 mice to assess the strain differences.
2016-04-15 | GSE80326 | GEO
Project description:The elaboration of a quality oocyte is integrally linked to the correct developmental progression of cumulus cell phenotype. In humans and non-human primates, oocyte quality is diminished with in vitro maturation. To determine the changes in gene expression in rhesus monkey cumulus cells (CC) that occur during the final day prior to oocyte maturation and how these changes differ between in vitro and in vivo maturation (IVM and VVM), we completed a detailed comparison of transcriptomes using the Affymetrix gene array. We observe a large number of genes differing in expression when comparing IVM-CC and VVM-CC directly, but a much larger number of differences comparing the transitions from the pre-oocyte maturation to post- IVM and post-VVM state. We observe a truncation or delay in the normal pattern of gene regulation, but also remarkable compensatory changes in gene expression during IVM. Among the genes affected in cumulus cells by IVM are those that contribute to productive cell-cell interactions between cumulus cell and oocyte and between cumulus cells. Numerous genes involved in lipid metabolism are incorrectly regulated during IVM, and the synthesis of sex hormones appears not suppressed during IVM. We identify a panel of 24 marker genes, the expression of which should provide the foundation for understanding how IVM can be improved, for monitoring IVM conditions, and for diagnosing oocyte quality. We compared transcriptomes of cumulus cells isolated from in vitro matured cumulus-oocyte complexes COCs (IVM-CC) and from in vivo matured COCs (VVM-CC) to identify potential cumulus cell markers of oocyte quality. The global gene expression profile of pre-maturation cumulus cells (PM-CC) was used to developmental transitions between IVM and VVM.
2011-05-22 | E-GEOD-25288 | biostudies-arrayexpress
Project description:MicroRNAs (miRNA) are important regulators of oocyte maturation, playing a key role in modulating gene expression both in a temporal- and spatial-specific manner. These small non-coding RNAs are involved in important processes during oocyte maturation, acting as messengers between the oocyte and its surrounding cumulus cells. Despite its significance, the bidirectional communication mechanism is still unknown. To test miRNA communication between oocyte and surrounding cumulus cells through the gap junctions the gap junctions were either blocked with carbenoxolone or not. MiRNA sequencing of oocytes at 1, 6, and 22 hours of in vitro maturation was then performed. Among the differentially expressed miRNAs, bta-miR-21-5p, a regulator of cumulus cell viability and oocyte maturation, was the only previously known miRNA. Furthermore, by labeling a bta-miR-21-5p mimic with FAM, crossing of this miRNA through the gap junctions within the cumulus-oocyte complex could be visualized and internalization in the oocyte was confirmed by RT-qPCR. In conclusion, this study provides, for the first time, evidence that miRNA communication within the bovine cumulus-oocyte complex is enabled through the gap junctional network.
2024-08-02 | GSE252748 | GEO
Project description:Changes in gene expression induced by FSH in cumulus cells treated with adenosine using Agilent EmbryoGENE microarray slides. Bovine cumulus-oocyte complexes in vitro-cultured for 6 h using adenosine. The effect of FSH was compared with control as non-treated cumulus-oocyte complexes. After culture, COC were were washed and cumulus cells were used for microarray analysis
2018-09-12 | GSE119803 | GEO
Project description:The maturation of an oocyte, the female gamete, during folliculogenesis is highly dependent on the molecular interaction with the somatic cells. Here we generated transcriptome data of single oocytes and the surrounding cumulus cells from antral follicles, and developed an analytical framework to unveil their inter-cellular communication. We identified hundreds of ligand-receptors pairs that can transduce paracrine signaling between oocyte and cumulus. Several of the ligand-coding genes expressed in oocytes and cumulus cells are also functionally associated with regulation of transcription. Ligand-coding genes expressed in oocytes or cumulus showed distinct enrichment for biological functions that are likely associated with a coordinated formation of the transzonal projections from the cumulus that reach the oocyte’s membrane. Finally, there were thousands of gene pairs with non-trivial linear co-expression pattern between oocytes and cumulus cells. Our analyses revealed a complex and functional regulatory circuit between the oocyte and surrounding cumulus cells.
2017-06-21 | GSE99678 | GEO
Project description:Triplicate samples of oocyte and cumulus cells were isolated from follicles of 2-8 mm, containing oocytes with several layers of cumulus cells were collected from ovaries. Proteins were extracted using DDF and digested using trypsin. The peptides were desalted, separated using in-line SCX-RPLC and analyzed using ion trap MS/MS. Proteins were identified using TurboSEQUEST 3.2
2011-04-15 | PRD000082 | Pride