Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

11 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Testis single-cell RNA-sequencing in the cynomolgus macaque reveals conserved transcriptional profiles during mammalian spermatogenesis

ABSTRACT: Spermatogenesis in mammals is a complex and highly orchestrated process, which involves the differentiation of diploid (2n-DNA content) spermatogonia into haploid (n) sperm. This process begins with spermatogonia, a niche of stem cells, which drive this process. Spermatogonial stem cells (SSCs) undergo mitotic self-renewal to maintain this niche, while sub-populations of spermatogonia progressively undergo differentiation and later gain competence to initiate meiosis and form sperm. SSCs undergo extensive chromatin remodelling and major morphological changes, while maintaining genome integrity and parental imprints. To study this in greater detail we performed single-cell RNA sequencing of spermatogenic cells derived from the testis of the non-human primate Macaca fascicularis.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Macaca fascicularis

SUBMITTER: Mahesh Sangrithi

PROVIDER: E-MTAB-8979 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Androgen Promotes Differentiation of Promyelocytic Leukemia Zinc Finger (PLZF)+ Spermatogonia pool via Indirect Regulatory Pattern

Project description:We examined a regulatory role of the AR during the process of spermatogenesis. Using a SSCs-Sertoli cells co-culture system, we demonstrated that androgen negatively regulated Plzf in SSCs that co-exist with Sertoli cells. In addition, we identified Gata2 as a target of AR in Sertoli cells, and subsequently observed that Wilms tumor 1 (WT1) and β1-integrin as two putative intermediate molecules to transfer the differentiation signals to SSCs. This signal pathway was further verified using androgen pharmacological deprivation mice model. These results demonstrate a regulatory pattern of androgen in SSCs niche, that androgen turns off the stemness maintenance switch PLZF in undifferentiated spermatogonia populations to promote spermatogenesis in an indirect way via multiple steps of signal transduction.

2019-02-28 | E-MTAB-7129 | biostudies-arrayexpress

The miRNA profiling of goat CD49f-positive and negative testicular cells

Project description:Purpose: miRNAs, a member of the small RNA, play critical roles in the mammalian spermatogenesis. Spermatogonia was the foundation of spermatogenesis and valuable for the study of spermatogenesis. However, it is still not clear that the expression profiling of the miRNAs in spermatogonia of dairy goat. Methods: The CD49f was one of the surface markers for spermatogonia enrichment by MACS. Therefore, we used CD49f microbeads antibody to purify CD49f-positive and negative cells of dairy goat testicular cells by MACS (Magnetic Activated Cell Sorting), and then in-depth analyzed the miRNA expression in these cells using Illumina sequencing technology. Results: The results of miRNAs expression profiling in purified CD49f-positive and negative testicular cells showed that 933 were miRNAs upregulated in CD49f-positive cells and 916 were miRNAs upregulated in CD49f-negative cells with a 2-fold increase, respectively; some spermatogonial stem cells(SSCs) specific miRNAs and marker genes in testis had a higher level expression in CD49f-positive testicular cells, such as miR-221, miR-23a, miR-29b, miR-24, miR-29a, miR-199b, miR-199a, miR-27a, miR-21. Conclusions: our comparative miRNAome data provided some useful miRNAs profiling data of dairy goat spermatogonia cells and suggested CD49f could be used to enrich dairy goat spermatogonia-like cells, including SSCs. miRNA profiles of goat CD49f-positive and negative testicular cells were generated by deep sequencing, in triplicate, using Illumina GAIIx

2014-04-25 | E-GEOD-57041 | biostudies-arrayexpress

Multiomics Approach to Profiling Development of the Spermatogonial Stem Cell Niche Focused on Sertoli cell Maturation

Project description:Spermatogonial stem cells are the foundation of spermatogenesis and as such can serve as a tool for the treatment of infertility in prepubertal cancer survivors. Spermatogonial stem cells are unique as they develop from primordial germ cells (PGCs), which colonize the developing tubules as immature SSC precursors. It has been controversial, when SSCs are maturing to an adult-like stem cell and recent research has found that prepubertal SSCs are actually metabolically distinct from adult SSCs until puberty. Sertoli cells picture a major part of the SSC niche and undergo drastic changes with puberty and polarize to compartmentalize the seminiferous epithelium with formation of tight junctions to a tight basal part where SSCs reside and an apical part with more differentiated stages of spermatogenesis. In the study were mapping the progression of Sertoli cells maturation events to the metabolic changes SSCs undergo during prepubertal development.

2023-02-24 | PXD037764 | Pride

Defining prepubertal primate spermatogonial stem cells to address fertility preservation in prepubertal boys

Project description:Antineoplastic treatments for cancer and other non-malignant disorders can result in male long-term or permanent infertility by ablating spermatogonial stem cells (SSCs). Preserving the future fertility of prepubertal patients faced with this prospect cannot rely on sperm banking. SSC transplantation using testicular tissue harvested before sterilizing treatment is a promising approach for restoring fertility, but lack of exclusive biomarkers which can unequivocally identify prepubertal SSCs in any primate species limits the therapeutic potential. To address this, we performed single-cell RNA-seq on unselected testis cells from immature baboons and macaques and compared these cells with published data from pre-pubertal human germ cells functionally-defined mouse SSCs. We found discrete groups of human spermatogonia while baboon and rhesus spermatogonia appeared less heterogenous. Cross-species analysis revealed cell types analogous to human SSCs in baboon and rhesus germ cells, but comparison with mouse SSCs revealed significant differences with primate SSCs. Indeed, a core component of a human SSC gene expression signature was conserved in baboon and rhesus spermatogonia and absent from mouse SSCs. These results further resolve the identity of pre-pubertal human SSCs and define novel pathways that could be leveraged for advancing their selection and propagation in vitro.

2023-05-15 | GSE222105 | GEO

Transcription and Imprinting Dynamics in Developing Postnatal Male Germline Stem Cells

Project description:Paternal imprinting initiates in primordial germ cells (PGCs), and is considered largely completed at birth. The resulting postnatal spermatogonial stem cells (SSCs) thenself-renew and proliferate to populate the testicular niche, with sexual maturation enabling productive gametogenesis. mRNA profiles of neonatal wild type (WT) mice testis were generated by deep sequencing using Illumina HiSeq 2000 Examination of 2 different histone modifications in mouse spermatogonia Please note that ChIPSeq_Kitplus samples are samples isolated with MACS CD117 microbeads from Miltenyi and ChIPSeq_Kitminus are samples that were not positively selected for Kit.

2015-11-09 | E-GEOD-62355 | biostudies-arrayexpress

Nucleome programming is required for the foundation of totipotency in mammalian germline development [Hi-C]

Project description:Germ cells are unique in engendering totipotency, yet the mechanisms underlying this capacity remain elusive. Here, we perform comprehensive and in-depth nucleome analysis of mouse germ-cell development in vitro, encompassing pluripotent precursors, primordial germ cells (PGCs) before and after epigenetic reprogramming, and spermatogonia/spermatogonial stem cells (SSCs). Although epigenetic reprogramming, including genome-wide DNA de-methylation, creates broadly open chromatin with abundant enhancer-like signatures, the augmented chromatin insulation safeguards transcriptional fidelity. These insulatory constraints are then erased en masse for spermatogonial development. Notably, despite distinguishing epigenetic programming, including global DNA re-methylation, the PGCs-to-spermatogonia/SSCs development entails further euchromatization. This accompanies substantial erasure of lamina-associated domains, generating spermatogonia/SSCs with a minimal peripheral attachment of chromatin except for pericentromeres—an architecture conserved in primates. Accordingly, faulty nucleome maturation, including persistent insulation and improper euchromatization, leads to impaired spermatogenic potential. Given that PGCs after epigenetic reprogramming serve as oogenic progenitors as well, our findings elucidate a principle for the nucleome programming that creates gametogenic progenitors in both sexes, defining a basis for nuclear totipotency.

2022-06-15 | GSE184129 | GEO

Nucleome programming is required for the foundation of totipotency in mammalian germline development [ChIP-Seq]

2022-06-15 | GSE183826 | GEO

Nucleome programming is required for the foundation of totipotency in mammalian germline development [NET-CAGE]

2022-06-15 | GSE183807 | GEO

Nucleome programming is required for the foundation of totipotency in mammalian germline development [ATAC-Seq]

2022-06-15 | GSE183801 | GEO

The histone demethylase KDM1A is essential for the maintenance and differentiation of spermatogonial stem cells and progenitors

Project description:Little is known of the fundamental processes governed by epigenetic mechanisms in the supplier cells of spermatogenesis, the spermatogonial stem cells (SSCs). The histone H3 lysine demethylase KDM1A is expressed in spermatogonia. We hypothesized that KDM1A serves in transcriptional regulation of SSCs and fertility. Using a conditional deletion of Kdm1a [conditional knockout (cKO)] in mouse spermatogonia, we determined that Kdm1a is essential for spermatogenesis as adult cKO males completely lack germ cells. Analysis of postnatal testis development revealed that undifferentiated and differentiating spermatogonial populations form in Kdm1a-cKO animals, yet the majority fail to enter meiosis. Loss of germ cells in the cKO was rapid with none remaining by postnatal day (PND) 21. To gain insight into the mechanistic implications of Kdm1a ablation, we isolated PND 6 spermatogonia enriched for SSCs and analyzed their transcriptome by RNA sequencing. Loss of Kdm1a was associated with altered transcription of 1206 genes. Importantly, differentially expressed genes between control and Kdm1a-cKO animals included those that are essential for SSC and progenitor maintenance and spermatogonial differentiation. The complete loss of fertility and failure to establish spermatogenesis indicate that Kdm1a is a master controller of gene transcription in spermatogonia and is required for SSC and progenitor maintenance and differentiation.

2019-02-16 | GSE126607 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data