Circulating-miRNAs expression profiles in an endangered Piedmontese sheep breed during the estrus cycle
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ABSTRACT:
PROVIDER: PRJNA1129860 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29653139.fastq.gz | Fastqsanger.gz | |||
| SRR29653140.fastq.gz | Fastqsanger.gz | |||
| SRR29653141.fastq.gz | Fastqsanger.gz | |||
| SRR29653142.fastq.gz | Fastqsanger.gz | |||
| SRR29653143.fastq.gz | Fastqsanger.gz |
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Project description:The preservation of locally endangered breeds is essential for ecosystem services that affect both society and the environment. Reproductive fitness becomes a crucial consideration in this regard. MicroRNAs (miRNAs) are small noncoding RNA molecules with a key role in post-transcriptional regulation. They usually act in tissues, where they are produced, but when released in extracellular fluid, they are termed circulating miRNAs (c-miRNAs). C-miRNAs might be potential biomarkers, whose profile changes under different physiological states. The purpose of this work is to establish a connection between distinctive variations in c-miRNAs’ expression and specific estrus cycle phases in Frabosana-Roaschina sheep, an endangered Piedmontese breed. Two trials of twenty ewes with different reproductive efficiency (nulliparous in the first trial, pluriparous in the second trial) were sampled on alternate days, after synchronization, for blood, saliva and feces. Ultrasound scans were performed during the induced estrus cycle. Animals were also video recorded to assess behaviors. Play behaviors and no sexual behaviors were detected in the first trial; sexual behaviors and no play behaviors in the second one. Based on plasma trends of 17β-estradiol and progesterone and ultrasound images, two moments were identified for miRNAs analyses: the beginning of the follicular phase (day 2) and the beginning of luteal phase (day 11). C-miRNAs of 6 representative animals from second trial were sent to be sequenced. Analyses on the sequencing data have highlighted twelve c-miRNAs differentially expressed (DE), comparing day 11 with day 2: five miRNAs resulted upregulated, whereas seven miRNAs are downregulated. An enrichment analysis, based on predicted targets, using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) databases was performed. Many of these genes regulate reproductive pathways with the possible involvement of miRNAs. In the end, qRT-PCR validation of DE miRNAs in all ewes was performed and differences in gene expression between the two sampling points and the two trials emerged, in line with literature. The investigation of these miRNAs’ involvement in the regulation of the estrus could improve reproductive performance and welfare of Frabosana-Roaschina.
2024-10-18 | GSE271102 | GEO
Project description:IntroductionThe preservation of locally endangered breeds is essential for maintaining ecosystem services that benefit both society and the environment. Reproductive fitness becomes a crucial consideration in this context. MicroRNAs (miRNAs) are small non-coding RNA molecules that play a key role in post-transcriptional regulation. Typically, they function within the tissues where they are produced. However, when they are released into extracellular fluid, they are referred to as circulating miRNAs (c-miRNAs). C-miRNAs may serve as potential biomarkers, whose profile changes under different physiological states. The purpose of this study is to establish a connection between distinctive variations in the expression of c-miRNAs and specific estrus cycle phases in Frabosana-Roaschina sheep, an endangered Piedmontese breed.MethodsTwo trials, each involving 20 ewes with different reproductive efficiencies (nulliparous in the first trial and pluriparous in the second trial), were sampled on alternate days after synchronization for blood, saliva, and feces. Ultrasound scans were performed during the induced estrus cycle. The animals' behaviors were assessed through video recordings.ResultsIn the first trial, play behaviors were detected without sexual behaviors, whereas in the second trial, sexual behaviors were observed without play behaviors. Based on plasma trends of 17β-estradiol and progesterone and ultrasound images, two moments were identified for miRNAs analyses: the beginning of the follicular phase (day 2) and the beginning of the luteal phase (day 11). C-miRNAs of six representative animals from the second trial were sequenced. Analyses of the sequencing data have identified 12 c-miRNAs that were differentially expressed (DE) when comparing day 11 with day 2: five miRNAs were found to be upregulated, whereas seven miRNAs were downregulated. An enrichment analysis, based on predicted targets, using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) databases was performed. Many of these genes regulate reproductive pathways with the possible involvement of miRNAs. Finally, qRT-PCR was conducted to validate the DE miRNAs in all ewes. Differences in gene expression between the two sampling points and the two trials were observed, in line with existing literature.DiscussionInvestigating the role of these miRNAs in regulating estrus could improve the reproductive performance and welfare of Frabosana-Roaschina ewes.
| S-EPMC11575464 | biostudies-literature
Project description:Background:The morphology of vaginal secretions during estrus and diestrus is characteristic and easy to distinguish. There are also significant differences in hormone levels between the two periods in physiological condition. However, the gene changes during estrus cycle especially the two periods are still unclear. Therefore, this study plans to find out the pathway changes related to the estrus cycle of female mice, the expression of various proteins, predict the genes sensitive to hormone changes in vivo through gene analysis of 15 tissues in the two periods and construct of differential gene expression library. Methods:The wildtype healthy female mice in estrus were compared with those in diestrus. The transcriptome changes between the two periods were probed by using high-throughput RNA-seq techniques. Results:A comprehensive mouse transcriptome map in estrus or diestrus across fifteen tissues including aorta, vein, brown adipose tissue, white adipose tissue, heart, kidney, liver, skeletal muscle, stomach, duodenum, cerebrum, hypothalamus, ovary, womb and spleen were provided. Conclusions:This dataset could serve as a baseline resource for investigating the potential gene changes sensitive to the estrus cycle across different tissues and provide the information for screening the key functional genes or molecular markers of estrus cycle.
2022-12-17 | GSE131172 | GEO
Project description:The current estrus detection method is generally time-consuming and has low accuracy. As such, a deeper understanding of the physiological processes during the estrus cycle accelerates the development of estrus detection efficiency and accuracy. This study used label-free acquisition mass spectrometry to explore salivary proteome profiles during the estrus cycle (day −3, day 0, day 3, and day 8) in pigs. A total of 1155 proteins were identified in the label-free analysis, of which 115 were identified as differentially expressed proteins (DEPs) among different groups (P ≤ 0.05). Functional annotation revealed that the DEPs were clustered in calcium ion binding, actin cytoskeleton, and lyase activity. Parallel reaction monitoring (PRM) was applied to verify the relative profiles of protein expression, in which PHB domain-containing protein, growth factor receptor-bound protein 2, elongation factor Tu, carboxypeptidase D, carbonic anhydrase, and trefoil factor 3 were confirmed to be consistent in both label-free and PRM approaches. Comparative proteomic assays on saliva would increase our knowledge of the estrus cycle in sows and provide potential methods for estrus detection.
2023-09-15 | PXD043141 | Pride
Project description:Vaginal and oral microbiota variation during estrus cycle
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Project description:We investigated the circulating microRNA expression profile of serum from sheep using microarray. In our study, we have six groups annotated as cyclic and pregnant, each group was divided into three subgroups including four animals in each group. We finally validated the microRNA of interest using qPCR.
2022-07-01 | E-MTAB-11709 | biostudies-arrayexpress
Project description:The potential for xenoestrogens and other environmental chemicals to alter female reproductive function calls for the study of their affects on endogenous hormone-regulated gene expression pathways during uterine tissue remodeling which occurs as part of the menstrual/estrus cycle. However, our knowledge of these pathways is limited. Here, we characterize changes in the CD-1 mouse uterine transcriptome during proestrus and estrus, which are regulated by estrogen and progesterone in preparation of the uterus for pregnancy. Mice were staged beginning at 6 wk of age and uterine horns were harvested after monitoring two estrus cycles. Microarray analysis identified 2,429 genes differentially expressed in estrus compared to proestrus, indicating that the mouse uterus undergoes remarkable remodeling during the estrus cycle, affecting ~10% of all protein-coding genes. Changes in gene expression associated with structural alteration of the uterus include remodeling of the extracellular matrix, changes in cell keratins and adhesion molecules, activation of mitosis, MHC class II presentation, complement and coagulation cascades, and cytochrome P450 expression. Signaling pathways regulated during the estrus cycle, involving ligand-gated channels, Wnt and hedgehog signaling, and several transcription factors with poorly understood roles in reproductive tissues, include several genes and gene networks that have been implicated in pathological states. The information presented here builds a background for understanding of mechanisms involved in uterine tissue response to endocrine disruptors and the development of reproductive tract diseases. Beginning on postnatal day 42, female CD-1 mice were monitored for reproductive stage cycle for 2 consecutive cycles and then total RNA was isolated from uterine horns at estrus or proestrus. Samples were pooled for microarray as follows. Six litters were used to generate 2 tissue pools for estrus and 2 tissue pools for proestrus, with estrus pool 1 and proestrus pool 1 comprised of mice from the same 3 litters, and estrus pool 2 and proestrus pool 2 comprised of mice from the other 3 litters. Each pool was comprised of uterine tissue RNA from n= 4-6 individual mice. Fluorescent labeling of RNA and hybridization of the Alexa 555-labeled (green) and Alexa 647-labeled (red) RNA samples to Agilent-026655 Whole Mouse Genome Microarray 4x44K v2 (Agilent Technology, Palo Alto, CA; catalog # G4846A) were carried out, with dye swapping for each estrus cycle stage comparison.
2013-06-07 | E-GEOD-43064 | biostudies-arrayexpress
Project description:The potential for xenoestrogens and other environmental chemicals to alter female reproductive function calls for the study of their affects on endogenous hormone-regulated gene expression pathways during uterine tissue remodeling which occurs as part of the menstrual/estrus cycle. However, our knowledge of these pathways is limited. Here, we characterize changes in the CD-1 mouse uterine transcriptome during proestrus and estrus, which are regulated by estrogen and progesterone in preparation of the uterus for pregnancy. Mice were staged beginning at 6 wk of age and uterine horns were harvested after monitoring two estrus cycles. Microarray analysis identified 2,429 genes differentially expressed in estrus compared to proestrus, indicating that the mouse uterus undergoes remarkable remodeling during the estrus cycle, affecting ~10% of all protein-coding genes. Changes in gene expression associated with structural alteration of the uterus include remodeling of the extracellular matrix, changes in cell keratins and adhesion molecules, activation of mitosis, MHC class II presentation, complement and coagulation cascades, and cytochrome P450 expression. Signaling pathways regulated during the estrus cycle, involving ligand-gated channels, Wnt and hedgehog signaling, and several transcription factors with poorly understood roles in reproductive tissues, include several genes and gene networks that have been implicated in pathological states. The information presented here builds a background for understanding of mechanisms involved in uterine tissue response to endocrine disruptors and the development of reproductive tract diseases.
2013-06-07 | GSE43064 | GEO
Project description:The potential for xenoestrogens and other environmental chemicals to alter female reproductive function calls for the study of their affects on endogenous hormone-regulated gene expression pathways during uterine tissue remodeling which occurs as part of the menstrual/estrus cycle. However, our knowledge of these pathways is limited. Here, we characterize changes in the CD-1 mouse uterine luminal epithelial cell transcriptome during proestrus and estrus, which are regulated by estrogen and progesterone in preparation of the uterus for pregnancy. Mice were staged beginning at 6 wk of age and uterine horns were harvested at estrus and proestrus. RNA was extracted from lumenal epithelium of uterine horns. Microarray analysis identified 2,251 genes differentially expressed in estrus compared to proestrus in lumenal epithelial cells. These complement other studies where RNA was extracted from whole uterine horns of mice in estrus and proestrus (GSE43064).
2013-06-07 | GSE46813 | GEO