Ontology highlight
ABSTRACT:
PROVIDER: PRJNA862464 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR20649222.fastq.gz | Fastqsanger.gz | |||
| SRR20649223.fastq.gz | Fastqsanger.gz | |||
| SRR20649224.fastq.gz | Fastqsanger.gz | |||
| SRR20649225.fastq.gz | Fastqsanger.gz | |||
| SRR20649226.fastq.gz | Fastqsanger.gz |
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Project description:While mature sperm is transcriptionally inactive, recent studies show that, following testicular its exit, the mammalian sperm acquires a load of small non-coding RNAs during transit in the epididymis, the last stage of sperm maturation. Importantly, this non-coding RNA load is sensitive to environmental insults.
2023-06-01 | GSE221431 | GEO
Project description:Spermatogenesis is a complex process, dependent upon the successive activation and/or repression of thousands of gene products, and ends with the production of haploid male gametes. RNA sequencing of male germ cells in the rat identified thousands of novel testicular unannotated transcripts, named TUTs. Although such RNAs are usually annotated as long non-coding RNAs, it is possible that some of these TUTs code for protein. To test this possibility, we used a “Proteomics Informed by Transcriptomics” strategy, combining shotgun proteomics analyses and RNA sequencing data for enriched populations of rat testicular cells. Among 3559 TUTs and 506 lncRNAs found in meiotic and post-meiotic germ cells, 44 encoded at least one peptide. We show that these novel high-confidence protein-coding loci exhibit several genomic features intermediate between those of lncRNAs and mRNAs. We experimentally validated the testicular expression pattern of two of these novel protein-coding gene candidates, both highly conserved in mammals: one for a vesicle-associated membrane protein, we named VAMP-9, and the other for an enolase domain-containing protein. This study confirms the potential of PIT approaches for the discovery of protein coding transcripts initially thought to be untranslated, or unknown transcripts. Our results contribute to the understanding of spermatogenesis by characterizing two novel proteins, implicated by their strong expression in germ cells.
2014-09-12 | PXD000872 | Pride
Project description:RNAs present in mature mammalian sperm are delivered to the zygote at fertilization, where they have the potential to affect early development. The biogenesis of the small RNA payload of mature sperm is therefore of great interest, as it may be a target of signaling pathways linking paternal conditions to offspring phenotype. Recent studies have suggested the surprising hypothesis that the small RNA payload carried by mature sperm may include RNAs that were not synthesized during testicular spermatogenesis, but that are instead delivered to sperm during the process of post-testicular maturation in the epididymis. To further test this hypothesis, we characterized small RNA dynamics during testicular and post-testicular germ cell maturation in mice, confirming and extending prior observations that testicular germ cell populations carry extremely low levels of tRNA fragments (tRFs), which only become highly abundant only after sperm have entered the epididymis. We examined the sperm RNA repertoire in greater detail, finding that the majority of 5’ tRNA fragments carry a 2’-3’ cyclic phosphate at their 3’ end, pointing to a role for RNaseA or T-family nucleases in tRNA cleavage in the male reproductive tract. The process of small RNA delivery to sperm can be recapitulated in vitro, as caput epididymosomes deliver small RNAs including tRFs and microRNAs to mature testicular spermatozoa. Finally, to definitively identify the tissue of origin for small RNAs in sperm, we carried out tissue-specific metabolic labeling of RNAs in intact mice, finding that mature sperm carry small RNAs that were originally synthesized in the somatic cells of the epididymis. Taken together, our data demonstrates that soma-germline small RNA transfer occurs in male mammals, most likely via vesicular transport from the epididymis to maturing sperm.
2018-07-15 | GSE112990 | GEO
Project description:Several observations have pointed a link between small RNA pathway and testicular germ cell tumorigenesis. Yet, the role of small RNAs in testicular germ cell tumors (TGCTs) is still not completely understood. In this study, we characterized the expression profiles of sRNAs in 9 primary sporadic TGCTs and 2 normal testes (NTs) using a sequencing approach. Our data show comprehensive coverage of microRNAs (miRNAs) expressed in human TGCT tissues and NTs, including the identification of 29 candidate novel miRNAs. We identified the differentially expression of miR-506~514 cluster and miR-21, miR-223 in the TGCTs compared to NTs. Functionally, we showed that miR-514a-3p positively regulates apoptosis through directly regulating PEG3. We further demonstrate that PEG3 activates NF-kappa B pathway in human testicular germ cell tumors.
2015-01-16 | GSE59267 | GEO
Project description:The somatic microenvironment supports spermatogonial stem cell differentiation into sperm. Extracellular matrix (ECM) plays multiple roles in the stem cell niche, including self-renewal, proliferation, differentiation and survival of spermatogonial cells. The pathophysiology of male infertility might be representative of a progressive degenerative process of the testicular tissue, including ECM, rather than a defective genetic background, thus outlining the existence of chronic etiological agents/pathways. In this context, we sought to identify potential causative factors responsible for a number of modifications of the testicular somatic microenvironment associated with idiopathic germ cell aplasia in human beings. Proteomic analysis of the decellularized ECM was performed to study testis parenchyma from 10 idiopathic non-obstructive azoospermic (iNOA) men, dichotomized according to positive sperm retrieval versus germ cell aplasia. Germ cell aplasia was characterized by an increased nuclear distribution of the retinoic acid receptor in Sertoli cells which was associated with decreased expression of the ECM markers, Nidogen-2 and Heparan sulfate proteoglycan-2. Decreased levels of the interstitial matrisome associated Factor IX and its regulator VKORC1 were instead coupled with decreased signaling of vitamin K in Leydig cells. This study identified pathogenetic signature of the somatic testicular microenvironment and provide mechanistic insights into the molecular determinants of human idiopathic germ cell aplasia.
2019-01-07 | PXD011817 | Pride
Project description:Extracellular vesicles (EVs) are known to contain important cargo of biologically active and regulatory molecules including small non-coding RNA (sncRNA). EVs from cauda epididymis play crucial role in post-testicular maturation of sperm. We assessed levels of cauda epididymosomes sncRNAs following exposure to low dose anti-androgenic Di-n-butyl phthalate (DBP), Di(2-ethylhexyl) phthalate (DEHP), and their mixtures in mice.
2025-10-13 | GSE267272 | GEO
Project description:RNA-seq analysis was conducted as part of an experiment investigating the effects of ethylene glycol monomethyl ether (EGME), on rat sperm RNA. EGME is a testicular germ cell toxicant that selectively targets spermatocytes. This experiment used an established model in which rats are treated with EGME by daily oral gavage for 5 days, with no additional treatment for 5 weeks, which is the time required for spermatocytes to become mature spermatozoa. The goal of the study was to test which small RNAs in rat sperm are altered following EGME exposure at doses below those that cause testicular histopathology. Testicular histopathology is observed at doses of 100 mg EGME/kg/d and above; this experiment included a dose range of 0 (vehicle), 50, 60, and 75 mg EGME/kg/d.
2025-12-10 | GSE313131 | GEO
Project description:Small non-coding RNA expression in murine germ cells
| PRJNA131953 | ENA
Project description:Interest in the sperm epigenome continues to grow in view of the realization that it is vulnerable to dynamic modifications arising from a variety of paternal environment exposures and that this legacy can serve as an important determinant of intergenerational inheritance. It has been postulated that such exchange may be communicated to maturing populations of spermatozoa via the transfer of small non-coding RNAs in a mechanism involving epididymosomes; small membrane bound vesicles secreted by the soma of the male reproductive tract (epididymis). Herein we confirm that mouse epididymosomes encapsulate an impressive repertoire of >350 microRNA (miRNA), a majority (~60%) of which are also represented in the miRNA signature of maturing spermatozoa. This includes >50 miRNAs that were found exclusively in epididymal sperm and epididymosomes, but not in the surrounding soma, thus supporting the notion that epididymosomes may selectively deliver regulatory non-coding RNA cargo to maturing sperm. Interestingly, we also documented substantial plasticity in terms of the epididymosome-borne miRNAs, including significant fold changes in the relative abundance of almost half of the miRNAs along the length of the epididymis. Finally, we provide the first direct evidence for the transfer of several prominent miRNAs between mouse epididymosomes and spermatozoa, and in so doing afford novel insight into a mechanism of intercellular communication through which the RNA payload of sperm can be modified during their post-testicular development. Examination of the microRNA expression profile of mouse epididymal epididymosomes using next generation sequencing in triplicate.
2016-08-25 | E-GEOD-79500 | biostudies-arrayexpress
Project description:This was a Phase II, open-label, non-randomized, multi-center study of oral dabrafenib in combination with oral trametinib in subjects with rare cancers harboring the BRAF V600E mutation including anaplastic thyroid cancer (ATC), biliary tract cancer (BTC), gastrointestinal stromal tumor (GIST), low grade (WHO G1/G2) glioma (LGG), high grade (WHO G3/G4) glioma (HGG), non-seminomatous germ cell tumors (NSGCT) / non-germinomatous germ cell tumors (NGGCT), adenocarcinoma of the small intestine (ASI), hairy cell leukemia (HCL) and multiple myeloma (MM).
| 2158616 | ecrin-mdr-crc