Transcriptomic analysis of human spermatogenesis
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ABSTRACT:
PROVIDER: PRJNA649963 | ENA |
REPOSITORIES: ENA
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Project description:Spermatogenesis generates mature male gametes and is critical for the proper transmission of genetic information between generations. However, the developmental landscape and underlying molecular signals during human spermatogenesis remain unknown. Here, we examined human spermatogenesis using transcriptome-wide single-cell RNA sequencing of 2,854 individual testicular cells from donors with normal spermatogenesis (donors with normal fertility or OA) and 174 testicular cells from one donor diagnosed as having nonobstructive azoospermia (NOA). Systematic bioinformatics analyses enabled us to delineate the full developmental trajectories of human spermatogenesis. A hierarchical model was established, which was characterized by the sequential and step-wise development of three spermatogonia subtypes, seven spermatocyte subtypes, and four spermatid subtypes. Furthermore, we recapitulated key hallmarks of human spermatogenesis at the single-cell level, including spermatogonial development, mitosis-to-meiosis transition, meiotic recombination, meiotic sex chromosome inactivation, and histone-to-protamine exchange. Remarkably, BMPR1B and FGFR3 were identified as novel markers of human spermatogonial stem cells, indicating the potentially critical role of BMP and FGF signaling pathways for SSC maintenance. Further analysis identified several novel marker genes of specific cell type such as HMGA1, PIWIL4, TEX29, SCML1, and CCDC112, the expression patterns of which were confirmed via RNA FISH or immunostaining. We also demonstrated that scRNA-seq provided a platform to find differentially expressed genes correlated with one type of nonobstructive azoospermia (NOA) at the genome-wide transcriptional profiling level, which might pave way for further diagnosis and dissecting the underlying mechanisms of male infertility. Our work allows for the reconstruction of transcriptional programs inherent to sequential cell fate transition during human spermatogenesis and has implications for deciphering male-related reproductive disorders.
2018-08-30 | GSE106487 | GEO
Project description:The Senegalese sole (Solea senegalensis) is a marine flatfish of high economic value and a target species for aquaculture. Here, we used a transcriptomic approach to investigate changes in genes expressed in the Senegalese sole testis throughout spermatogenesis in wild-caught fish adapted to captivity. We identified approximately 400 genes that are differentially expressed during the progression of spermatogenesis and that participate in processes such as activation of the ubiquitin-proteasome system, sperm maturation and motility, cell adhesion or cytoskeletal remodeling. The results from this study contribute to our understanding of the molecular changes ocurring during spermatogenesis in the Senegalese sole. This study represents spermatogenesis in Solea senegalensis: mid versus late spermatogenesis. Total RNA from testes at different stages in spermatogenesis (early, mid, late and functional maturation) from F0 wild Senegalese sole (3-4 animals at each stage) was extracted using the RNeasy extraction kit (Qiagen) and treated with DNAse following the manufacturer’s instructions. Quantitative and qualitative analysis of total RNA was performed using the Agilent 2100 bioanalyzer. RNA samples from each stage were pooled and amplified, labelled and hybridized to a custom-made oligonucleotide microarray containing 5,087 Senegalese sole Unigene sequences. In brief, pooled testicular RNAs from each stage were amplified and the resulting cRNAs labelled with Cy3 and Cy5, respectively, mixed in equal amounts and hybridized to the microarray for 17 h at 60 ºC.
2010-05-07 | E-GEOD-21637 | biostudies-arrayexpress
Project description:Transcriptomic analysis of hypersegmented human neutrophils
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Project description:The Senegalese sole (Solea senegalensis) is a marine flatfish of high economic value and a target species for aquaculture. Here, we used a transcriptomic approach to investigate changes in genes expressed in the Senegalese sole testis throughout spermatogenesis in wild-caught fish adapted to captivity. We identified approximately 400 genes that are differentially expressed during the progression of spermatogenesis and that participate in processes such as activation of the ubiquitin-proteasome system, sperm maturation and motility, cell adhesion or cytoskeletal remodeling. The results from this study contribute to our understanding of the molecular changes ocurring during spermatogenesis in the Senegalese sole. This study represents spermatogenesis in Solea senegalensis: functional mature versus late spermatogenesis. Total RNA from testes at different stages in spermatogenesis (early, mid, late and functional maturation) from F0 wild Senegalese sole (3-4 animals at each stage) was extracted using the RNeasy extraction kit (Qiagen) and treated with DNAse following the manufacturer’s instructions. Quantitative and qualitative analysis of total RNA was performed using the Agilent 2100 bioanalyzer. RNA samples from each stage were pooled and amplified, labelled and hybridized to a custom-made oligonucleotide microarray containing 5,087 Senegalese sole Unigene sequences. In brief, pooled testicular RNAs from each stage were amplified and the resulting cRNAs labelled with Cy3 and Cy5, respectively, mixed in equal amounts and hybridized to the microarray for 17 h at 60 ºC.
2010-05-07 | E-GEOD-21635 | biostudies-arrayexpress
Project description:The Senegalese sole (Solea senegalensis) is a marine flatfish of high economic value and a target species for aquaculture. Here, we used a transcriptomic approach to investigate changes in genes expressed in the Senegalese sole testis throughout spermatogenesis in wild-caught fish adapted to captivity. We identified approximately 400 genes that are differentially expressed during the progression of spermatogenesis and that participate in processes such as activation of the ubiquitin-proteasome system, sperm maturation and motility, cell adhesion or cytoskeletal remodeling. The results from this study contribute to our understanding of the molecular changes ocurring during spermatogenesis in the Senegalese sole. This study represents spermatogenesis in Solea senegalensis: early versus late spermatogenesis. Total RNA from testes at different stages in spermatogenesis (early, mid, late and functional maturation) from F0 wild Senegalese sole (3-4 animals at each stage) was extracted using the RNeasy extraction kit (Qiagen) and treated with DNAse following the manufacturer’s instructions. Quantitative and qualitative analysis of total RNA was performed using the Agilent 2100 bioanalyzer. RNA samples from each stage were pooled and amplified, labelled and hybridized to a custom-made oligonucleotide microarray containing 5,087 Senegalese sole Unigene sequences. In brief, pooled testicular RNAs from each stage were amplified and the resulting cRNAs labelled with Cy3 and Cy5, respectively, mixed in equal amounts and hybridized to the microarray for 17 h at 60 ºC. Each hybridization was performed at least in duplicate.
2010-05-07 | E-GEOD-21634 | biostudies-arrayexpress
Project description:Spermatogenesis is a complex and highly orchestrated combination of processes in which male germline proliferation and differentiation result in the production of mature spermatozoa. If recent genome-wide studies have contributed to the in-depth analysis of the male germline protein-coding transcriptome, little effort has yet been devoted to the systematic identification of lncRNAs expressed during spermatogenesis in human. We report high-resolution expression profiling of human male germ cells using Illumina next-generation sequencing technology and highly enriched testicular cell populations. 25,161 high-confidence transcripts were reconstructed and classified into eleven expression patterns. Our study provides new insights in transcriptional profiling of the male germline and represents a high-quality resource of novel loci expressed during spermatogenesis that significantly contributes to the human genome annotation. A graphical display of the data is conveniently accessible through the ReproGenomics Viewer (RGV) at http://rgv.genouest.org.
2017-11-24 | GSE74896 | GEO