10x genomics single cell sequencing of yak testis at different developmental stages
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ABSTRACT:
PROVIDER: PRJNA1083907 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28229653_1.fastq.gz | Fastqsanger.gz | |||
| SRR28229653_2.fastq.gz | Fastqsanger.gz | |||
| SRR28229654_1.fastq.gz | Fastqsanger.gz | |||
| SRR28229654_2.fastq.gz | Fastqsanger.gz | |||
| SRR28229655_1.fastq.gz | Fastqsanger.gz |
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Project description:Testis is the most important reproductive organ of men, and the integrity of its physiological function is crucial for the successful production of sperm. In this study, single-cell RNA sequencing technology was used to construct cell expression profiles of yak at different developmental stages and adult cattle-yak testicular tissues. The identification results of cell subsets and marker genes were analyzed, and the possible mechanisms were predicted.
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Project description:10x genomics single cell sequencing of yak testis
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Project description:Hair follicles of the yak are in anagen and catagen , the hair follicles of healthy female yaks around 2 years old are collected for the preparation of single-cell suspension, the cells were sequenced by scRNA-seq on the 10x genome platform. A total of about 12000 single-cell transcriptome information were obtained. According to the reported marker genes, the main cell groups in anagen and catagen of yak were identified. Based on the analysis of pseudotime trajectory, the differentiation trajectory of epidermal cell lineage and dermal cell lineage during hair follicle development and the dynamic changes of genes during differentiation were described.
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Project description:Studying spermatogenesis is the key to understanding the development mechanism of the yak reproductive system. Although N6-methyladenosine (m6A) RNA modification has been reported to regulate spermatogenesis and reproductive function in mammals, the molecular mechanism of m6A in yak testis development and spermatogenesis remains largely unknown. Therefore, we collected testicular tissue from junile and adult yaks, and found that the m6A level significantly increased after sexual maturity in yak. In MeRIP-seq, 1,702 hypermethylated peaks and 724 hypomethylated peaks were identified. The hypermethylated differentially methylated RNAs (DMRs) (CIB2, AK1, FOXJ2, PKDREJ, SLC9A3, and TOPAZ1) mainly regulated spermatogenesis, while the hypomethylated DMRs (BCL6, USP25, CD96, EPHA2, and TAF12) mainly participated in immune response. Functional enrichment analysis showed that DMRs were significantly enriched in the adherens junction, gap junction, and Wnt, PI3K, and mTOR signaling pathways, regulating cell development, spermatogenesis, and testicular endocrine function. The functional analysis of differentially expressed genes showed that they were involved in the biological processes of mitosis, meiosis, and flagellated sperm motility during sexual maturity of yak testis. We also screened the key regulatory factors of testis development and spermatogenesis by combined analysis, which included BRCA1, CREBBP, STAT3, and SMAD4. This study has important research value and practical guiding significance for yak genetic improvement, particularly in understanding the molecular mechanism and evolutionary dynamics of the progression of testis developmental stages in yaks.
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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.
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Project description:10x genomics single cell sequencing of yak hair follicle
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Project description:10X genomics single cell sequencing of sheep testis
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Project description:10X genomics single cell sequencing of sheep testis
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Project description:N6-methyladenosine (m6A) is the most common internal modification of eukaryotic mRNA, and its potential regulatory role has recently been identified in mammals, plants, and yeast. However, little is known about the role of m6A methylation in mammalian sexual maturation. In this study, the testicular tissue of yaks before and after sexual maturation was taken as the research object, and the m6A map of testicular tissue of yaks before and after sexual maturation was obtained through the preliminary experiment and MERIP-seq. The results showed that only spermatogonial cells and some primary spermatocytes could be seen in the testicular tissue of yak before sexual maturation, while spermatogenic cells at different stages could be seen in the testicular tissue after sexual maturation. It was found that the methylation level was higher after sexual maturation than before by detecting the expression of methylation related enzymes and the overall methylation level of testis. There were 1438 differential methylation peaks before and after sexual maturation, of which 1226 were significantly up-regulated and 212 were significantly down-regulated after sexual maturation. Through annotation, it was found that the differential methylation peaks were mainly concentrated in the exon region, followed by 3'UTR, and finally 5'UTR. KEGG pathway analysis showed that Homologous recombination, Notch signaling pathway, Growth hormone synthesis and other signaling pathways may be related to testicular development and maturation. m6A modification was positively correlated with mRNA abundance, suggesting that m6A plays a regulatory role in mammalian sexual maturation. In this study, we reported for the first time the m6A transcriptional map of yak testis, providing a starting point for revealing the function of m6A that may affect the development of yak testis.
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