Circular RNA Expression and Regulation Profiling in Testicular Tissues of Immature and Mature Wandong Cattle (Bos taurus)
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA760322 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15711831_1.fastq.gz | Fastqsanger.gz | |||
| SRR15711831_2.fastq.gz | Fastqsanger.gz | |||
| SRR15711832_1.fastq.gz | Fastqsanger.gz | |||
| SRR15711832_2.fastq.gz | Fastqsanger.gz | |||
| SRR15711833_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
Similar Datasets
Project description:Wandong cattle are an autochthonous Chinese breed used extensively for beef production. The breed tolerates extreme weather conditions and raw feed and is resistant to tick-borne diseases. However, the genetic basis of testis development and sperm production as well as breeding management is not well established in local cattle. Therefore, improving the reproductive efficiency of bulls via genetic selection is crucial as a single bull can breed thousands of cows through artificial insemination (AI). Testis development and spermatogenesis are regulated by hundreds of genes and transcriptomes. However, circular RNAs (circRNAs) are the key players in many biological developmental processes that have not been methodically described and compared between immature and mature stages in Bovine testes. In this study, we performed total RNA-seq and comprehensively analyzed the circRNA expression profiling of the testis samples of six bulls at 3 years and 3 months of developmental age. In total, 17,013 circRNAs were identified, of which 681 circRNAs (p-adjust < 0.05) were differentially expressed (DE). Among these DE circRNAs, 579 were upregulated and 103 were downregulated in calf and bull testes. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that the identified target genes were classified into three broad functional categories, including biological process, cellular component, and molecular function, and were enriched in the lysine degradation, cell cycle, and cell adhesion molecule pathways. The binding interactions between DE circRNAs and microRNAs (miRNAs) were subsequently constructed using bioinformatics approaches. The source genes ATM, CCNA1, GSK3B, KMT2C, KMT2E, NSD2, SUCLG2, QKI, HOMER1, and SNAP91 were found to be actively associated with bull sexual maturity and spermatogenesis. In addition, a real-time quantitative polymerase chain reaction (RT-qPCR) analysis showed a strong correlation with the sequencing data. Moreover, the developed model of Bovine testes in the current study provides a suitable framework for understanding the mechanism of circRNAs in the development of testes and spermatogenesis.
| S-EPMC8647812 | biostudies-literature
Project description:The mature and immature FF samples were subjected to mass spectrometry with the isobaric tags for relative and absolute quantification (iTRAQ). The differential proteomics between mature and immature FF revealed their striking differences in the protein components and functions, which may improve our knowledge of the follicular microenvironment and its biological roles for reproductive processes in yak.
2021-04-15 | PXD025426 |
Project description:Wandong cattle are an autochthonous Chinese breed used extensively for beef production. The breed tolerates extreme weather conditions and raw feed and are resistant to tick-borne diseases. However, the genetic basis of testis development and sperm production as well as breeding management is not well established in local cattle. In this study, we performed total RNA-Seq and comprehensively analyzed the circ-RNA expression profiling of the testes samples of six bulls at 3 years and 3 months of developmental age. In total, 17 013 circ-RNAs were identified, of which 681 circRNAs (P-adjust < 0.05) were differentially expressed (DE). Among these DE circ-RNAs, 579 were upregulated and 103 were downregulated in calf and bull testes. The Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that the identified target genes were classified into three broad functional categories, including biological process, cellular component, and molecular function, and were enriched in the lysine degradation, cell cycle, and cell adhesion molecule pathways.
2021-09-05 | GSE183347 | GEO
Project description:We report screening of genes differentially expressed in cells isolated from immature and mature third molar teeth. Among them, a homeobox transcription factor, distal-less homeobox 4 (DLX4) was highly expressed in immature human dental pulp cells, and significantly enhanced iPSC colony formation in combination with OCT3/4, SOX2, and KLF4 to the level comparable with that using classical combination of Yamanaka's factors, OCT3/4, SOX2, KLF4, and c-MYC.
2014-12-25 | GSE52853 | GEO
Project description:Filarial nematodes are arthropod-borne nematodes that cause a variety of economically important diseases such as onchocerciasis (river blindness), lymphatic filariasis, and heartworm disease. The most widespread filarial disease of humans is lymphatic filariasis, caused by worms in the genera Wuchereria and Brugia. Lymphatic filariasis is an economic and social burden in endemic countries and affects approximately 119 million people worldwide (Michael, 1997). In humans, the worms live in and block the lymph vessels, causing improper flow of lymph, and inflammation of the lymphatic system. The symptoms are fever, swollen limbs and genitals, generalized malaise, and can progress to a debilitating condition known as elephantiasis This research focuses on the transmission of these worms to the disseminating mosquito host, and it is based on the interesting observation that mf must be at least 7 days old to successfully infect the mosquito (de Hollanda, 1982). Newborn mf that have not â??maturedâ?? cannot successfully penetrate the midgut of the mosquito, and subsequently cannot develop to the L3 stage (Fuhrman, 1987). Previous work done by another group 20 years ago suggests that the molecular makeup of the worm surface changes during this maturation process (Furman, 1983 a and b). We used microarray analysis to characterize changes in gene expression that take place during the mf maturation process. Understanding the gene expression changes that occur as the mf mature will allow us to understand the nature of the philological transition that allows mf to move from the human to the mosquito host. With this information in hand, we can eventually identify parasite molecules that could be targeted to either stop parasite reproduction or prevent transmission of the mf to the mosquito. This would stop parasite transmission in endemic areas. This SuperSeries is composed of the following subset Series: GSE14939: Brugia pahangi mature vs immature microfilariae GSE14940: Brugia malayi mature vs immature microfilariae Refer to individual Series
2009-10-01 | E-GEOD-15017 | biostudies-arrayexpress
Project description:To understand the etiology behind higher incidence of infertility in crossbred bulls, we performed transcriptomic analysis of testicular samples derived from crossbred males and compared with testicular transcriptomic profile of Zebu cattle
2020-07-08 | GSE153952 | GEO
Project description:Immature dentate granule cells (DGCs) generated in the hippocampus during adulthood are believed to play a unique role in dentate gyrus function. Although immature DGCs have hyperexcitable membrane properties in vitro, the consequences of this hyperexcitability in vivo remain unclear. In particular, the relationship between experiences that activate the dentate gyrus, such as exploration of a novel environment (NE), and downstream molecular processes that modify dentate gyrus circuitry in response to cellular activation are unknown in this cell population. We first performed quantification of immediate early gene proteins in immature (5-week-old) and mature (13-week-old) DGCs from mice exposed to a NE. Paradoxically, we observed lower immediate early gene protein expression in hyperexcitable immature DGCs. We then isolated nuclei from active and inactive immature DGCs and performed single nuclei RNA-Sequencing. Compared to mature nuclei collected from the same animal, immature DGC nuclei showed less activity-induced transcriptional change, even though they were classified as active based on expression of ARC protein. These results demonstrate that the coupling of spatial exploration, cellular activation, and transcriptional change differs between immature and mature DGCs, with blunted activity-induced changes in immature cells.
2023-02-23 | GSE214309 | GEO
Project description:In this study, we explored gene expression profiles of mature and immature basophils from either IL-3-elicited or TSLP-elicited BMBAs. We revealed that TSLP-elicited mature basophils displayed gene expression profile similar to that of IL-3-elicited mature rather than immature basophils.
2023-03-21 | GSE206592 | GEO
Project description:Mass spectrometry study of interactor binding to the EVH1 domain of VASP in mature and immature dendritic cells. We performed mass spectrometry study using a specially designed inhibitor that recognizes this characterized motif with high affinity and analyzed the digested peptides by LC-MS. For both, iDCs and mDCs, two independent experiments were carried out (N=2). As control for the specificity of the identified interactions an additional two independent experiments (N=2) were carried out for both, iDCs and mDCs, where a specific inhibitor of the EVH1 domain was added to outcompete bona fide EVH1 domain interactions.
2022-10-20 | PXD030882 | Pride