Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR30675300_1.fastq.gz | Fastqsanger.gz | |||
| SRR30675300_2.fastq.gz | Fastqsanger.gz | |||
| SRR30675301_1.fastq.gz | Fastqsanger.gz | |||
| SRR30675301_2.fastq.gz | Fastqsanger.gz | |||
| SRR30675302_1.fastq.gz | Fastqsanger.gz |
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Project description:Cattle-yak is the hybrid offspring of yak and cattle. It has obvious heterosis in production performance, but the male sterility of cattle-yak has always been the focus of attention. Studies have shown that non-coding RNA is involved in the regulation of spermatogenesis. We comprehensively compared the testicular transcription profiles of cattle, yak and cattle-yak. More DEGs, DECs and DEMs were found in the intersection of the two comparison groups of cattle and cattle-yak, yak and cattle-yak, with 4,968, 360 and 59, respectively. The DEGs of cattle-yak, cattle and yak were mainly enriched in biological processes such as spermatogenesis, male gamete generation and sexual reproduction. At the same time, GO and KEGG analysis suggested that DECs host genes and DEMs source genes were also involved in the regulation of spermatogenesis. The construction of potential ceRNA networks found that some differentially expressed ncRNAs may be involved in the regulation of genes related to testicular spermatogenesis, including miR-423-5p, miR-449b, miR-34b/c, miR-15b, etc., as well as unreported miR-6123, miR-1306 and some miRNA and circRNA interaction pairs. This study provides a reference for further study on the mechanism of male sterility in cattle-yak.
2024-02-06 | GSE254886 | GEO
Project description:To investigate the potential effect of grazing movement on miRNA circulation in cattle, here we profiled miRNA expression in centrifugally prepared exosomes from the plasma of both grazing and housed Japanese Shorthorn cattle. Microarray analysis of the c-miRNAs resulted in detection of a total of 231 bovine exosomal miRNAs in the plasma, with a constant expression level of let-7g across the duration and cattle groups. Expression of muscle-specific miRNAs such as miR-1, miR-133a, miR-206, miR-208a/b, and miR-499 were undetectable, suggesting the mildness of grazing movement as exercise.
2016-01-01 | GSE69717 | GEO
Project description:To investigate the potential effect of grazing movement on miRNA circulation in cattle, here we profiled miRNA expression in centrifugally prepared exosomes from the plasma of both grazing and housed Japanese Shorthorn cattle. Microarray analysis of the c-miRNAs resulted in detection of a total of 231 bovine exosomal miRNAs in the plasma, with a constant expression level of let-7g across the duration and cattle groups. Expression of muscle-specific miRNAs such as miR-1, miR-133a, miR-206, miR-208a/b, and miR-499 were undetectable, suggesting the mildness of grazing movement as exercise. Changes in miRNA expression in plasma exosome of cattle was measured at during 0, 1, 2 and 4 months of grazing or housing. Plasma exosome samples prepared from three cattle for each treatment were collected and mixed within the treatment at each time for microarray analysis .
2016-07-03 | E-GEOD-69717 | biostudies-arrayexpress
Project description:This study explores how yaks, an ideal animal model for studying plateau adaptability, adapt to high-altitude environments. The lung is a representative organ of the yak’s adaptation to high-altitude environments. The F1 hybrids of yak and cattle, known as dzho, also exhibit adaptability to plateau conditions. This study constructed a single-cell transcriptome atlas of the lungs in yak, dzho and cattle, containing 51 subtypes. We initially found that the differential subtypes among yak, dzho and cattle were mainly concentrated in T&NK cells and fibroblasts. Most of them belonged to new cell subtypes. Subsequently, we speculated that NKG7 and CD4 played a central regulatory role in T&NK cells, contributing to T cell activation and affecting the adaptive immune response of yaks. In fibroblasts, MYL9 and IGF2 are believed to play key regulatory roles, participating in maintaining cellular energy metabolism balance. These results provide an important scientific basis for systematically analysing the molecular regulatory mechanisms of yak adaptation to high-altitude hypoxia.
2024-05-03 | GSE266061 | GEO
Project description:N6-methyladenosine (m6A) is the most prominent mRNA modification in eukaryotes, and its potential regulatory role has recently been identified in mammals, plants, and yeast. However, how m6A methylation regulates spermatogenesis remains unknown. In this study, cattle-yak testis tissue was used as the experimental material, and the m6A map was generated through preliminary experiments and methylated RNA immunoprecipitation sequencing. Only spermatogonia and Sertoli cells were observed in cattle-yak testis tissue. Experiments examining the expression of methylation-related enzymes and the overall methylation level showed that the methylation level in the testis of the cattle-yak was slightly lower than that of the sexually mature yak, but significantly higher than that of the pre-sexually mature yak. Annotation analysis indicated that differentially methylated peaks were most frequently concentrated in exonic regions, followed by 3'UTR and finally 5'UTR regions. Through enrichment analysis of differentially expressed genes and differentially methylated corresponding genes, GO analysis of T-vs-Y group mainly involved spermatogenesis, including cytoskeleton, actin binding, etc. KEGG analysis showed that the differential genes were mainly enriched in actin cytoskeleton regulation and MAPK signaling pathway. GO analysis of the T-vs-M group mainly involved protein ubiquitination, ubiquitin ligase complexes, ubiquitin-dependent protein catabolism and endocytosis. KEGG analysis mainly involved apoptosis and Fanconi anemia pathways. This study will lay the foundation for elucidating the molecular mechanism of m6A in male sterility of cattle-yak.
2022-06-12 | GSE205649 | GEO
Project description:Purpose：Yak long-term colonization and widespread distribution across the plateau can be serve as an ideal natural animal model to provide insights into the adaptive evolution of other plateau species, including humans. Methods:To exploring the molecular mechanisms of lung tissue in yak to response to hypoxia, the mRNA, lncRNA and miRNA of lung tissue from cattle and three different altitude yaks were sequenced. Results:A total of 21764 mRNAs, 14168 lncRNAs and 1209miRNAs (305 known and 904 novel miRNAs)were identifed.Compared yak with cattle, 4975 mRNAs, 3326 lncRNAs and 75 miRNAs were differentially expressed. 756 mRNAs, 346 lncRNAs and 83 miRNAs were found to be differentially expressed amongthree different altitude yaks(fold change≥2 and P-value<0.05). Conclusions:The differentially expressed genes were functionally enriched in long-chain fatty acid metabolic process and protein processing between yak and cattle, while the immune response and cell cycle were enriched among three different altitude yaks. Furthermore, the competing endogenous RNAs (ceRNAs) networks were identified to illustrate their roles.
2020-07-08 | GSE153962 | GEO
Project description:This study used yak and cattle-yak testes from different developmental stages as materials to construct a complete translation map of the testes, and integrated transcriptome and translation results to explore gene expression changes during the sexual maturation process of yak testes. This study utilized Ribo seq technology to construct a transcriptome map of yak testicular development, revealing that the expression of genes related to spermatogenesis is specifically translated and regulated at different developmental stages. In addition, many unknown open reading frames (ORFs) in the testes have been newly identified.
2024-08-30 | GSE270057 | GEO
Project description:Sex condition has been demonstrated to alter meat quality and sex is a major factor that affects the fatty acid composition of lipids of carcass dissectible or intramuscular depot fats. But the possible genetic molecular mechanism of gender causing meat quality differences is not well defined. Qinchuan cattle, Qinghai yak and Guangxi buffalo are three typical indigenous species of cattle in China. Obivious differences of meat quality exist among the three species of cattle. Few studies have been conducted to elucidate the muscle tissue expression of genes involved in pathways and mechanisms leading to meat quality differences beyond the phenotype properties of beef. Bovine Genome Arrays were used to construct muscle expression profiles of the longuissimus dorsi from Qinchuan cattle at 36 months and screen differentially expressed genes in the longuissimus dorsi muscle tissues among different genders of Qinchuan cattle, between Qinchuan cattle and Qinghai yak, and between Qinchuan cattle and Guangxi buffalo.
2009-12-23 | GSE19586 | GEO
Project description:Neotyphodium coenophialum is an endophytic fungus that infects most tall fescue (Festuca arundinacea) pastures that are commonly used in animal grazing systems in the United States. Beef cattle grazing such pastures are impaired in health and production performance, resulting in a large economic loss in US food-animal production systems. Based on the clinical symptoms and laboratory analyses of blood, it was hypothesized that such affected cattle display liver-specific changes in the expression of gene transcripts that are associated with the metabolic enzymes and transporters critical for beef health and performance. Microarray analysis using the GeneChip Bovine Genome Array (Affymetrix, Inc., Santa Clara, CA) was conducted to determine if grazing endophyte-infected tall fescue pastures affects the liver gene expression profiles of growing beef steers.
2010-11-30 | GSE23894 | GEO
Project description:Purpose：Yak long-term colonization and widespread distribution across the plateau can be serve as an ideal natural animal model to provide insights into the adaptive evolution of other plateau species, including humans. Methods:To exploring the molecular mechanisms of lung tissue in yak to response to hypoxia, the mRNA, lncRNA and miRNA of lung tissue from cattle and three different altitude yaks were sequenced. Results:A total of 21764 mRNAs, 14168 lncRNAs and 1209miRNAs (305 known and 904 novel miRNAs)were identifed.Compared yak with cattle, 4975 mRNAs, 3326 lncRNAs and 75 miRNAs were differentially expressed. 756 mRNAs, 346 lncRNAs and 83 miRNAs were found to be differentially expressed amongthree different altitude yaks(fold change≥2 and P-value<0.05). Conclusions:The differentially expressed genes were functionally enriched in long-chain fatty acid metabolic process and protein processing between yak and cattle, while the immune response and cell cycle were enriched among three different altitude yaks. Furthermore, the competing endogenous RNAs (ceRNAs) networks were identified to illustrate their roles.
2020-07-08 | GSE153956 | GEO