Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chromatin States in Murine Spermatogonia

ABSTRACT: We report ATAC-seq analysis throughout spermatogonial development. We have assayed two biological replicates at 0, 18, 48, and 120 hours post WIN 18,446/RA treatment.

ORGANISM(S): Mus musculus

PROVIDER: GSE197484 | GEO | 2023/03/03

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

RNA-seq Analysis of spermatogonia with NRRA treatment Transcriptomes [Veh.vs.NRRA]

Project description:Purpose: The goals of this study are to compare RA, NR and NRRA treatment in in vitro spermtogonia transcriptome profiling (RNA-seq) and to evaluate protocols for in vitro induced meiosis system. Methods: Spermatogonia mRNA profiles of Veh, RA, NR and NRRA were generated by deep sequencing, in duplicate. Conclusions: Our study represents the first detailed analysis of induced meiosis spermatogonia transcriptomes, with biologic replicates, generated by RNA-seq technology.

2021-02-16 | GSE153271 | GEO

10x Genonics single-cell RNA-seq of immature (P6) ID4-EGFP mouse spermatogonia & testis cells

Project description:To reveal distinct transcriptomes associated with spermatogonial stem cell renewal vs. initiation of differentiation, single-cell transcriptomes from P6 ID4-EGFP+ spermatogonia (sorted for brightest or dimmest) or unselected testis cells were used for Drop-Seq analysis. The GFP-bright and dim phenotypes exhibit distinct fates when assayed by transplantation, with ID4-EGFPbright cells highly enriched for SSCs, and ID4-EGFPdim cells enriched for progenitors. We used the 10x Genomics Chromium (a commercial Drop-Seq variant) to perform single-cell RNA-seq

2018-11-06 | GSE109049 | GEO

Retinoic acid dependent spermatogonial differentiation in mice

Project description:Spermatogonial differentiation is a developmental process that is essential for spermatogenesis, but the molecular and cellular changes that germ cells must undergo to transition from undifferentiated spermatogonia to differentiating spermatogonia remain largely undefined. Retinoic acid (RA) is necessary and sufficient for spermatogonial differentiation. Using the postnatal mouse testis, we examine the transcriptome changes that accompany spermatogonial differentiation. Spermatogenesis was synchronized by administration of potent and selective RA synthesis inhibitor; as a result, testes contained only undifferentiated spermatogonia. Then, the inhibitor was discontinued, and mice were given a single dose of exogenous RA to initiate spermatogonial differentiation. We measured transcriptomes in FACS-enriched germ cells either before RA administration, when the cells correspond to Aal spermatogonia (and a minor contribution of spermatogonial stem cells) or at two points after RA administration, when the cells correspond to A1 or A3 differentiating spermatogonia. The results of this study reveal the full transcriptome changes accompanying spermatogonial differentiation in the mouse.

2023-07-03 | GSE213716 | GEO

Comprehensive molecular characterization of the soybean rust disease [Embrapa-Soja - Iowa State Univ; 2005]

Project description:Experimental design: 2 genotypes: PI230970 (resistant USDA Plant Introduction (PI) line containing SBR Rpp2 resistance gene) & Embrapa-48 (susceptible Brazilian cultivar) 2 treatments: Soybean rust challenge & mock infection 3 replications 10 time points: 6, 12, 18, 24, 36, 48, 72, 96, 120, 168hai TOTAL: 120 Affymetrix GeneChip(R) Soybean Genome Arrays ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Martijn van de Mortel. The equivalent experiment is GM2 at PLEXdb.]

2011-11-22 | GSE33410 | GEO

Adult mouse stage synchronized testis array

Project description:WIN 18,446/RA treatment of neonatal male mice was used to synchronize spermatogenesis to 2-3 different stages of the cycle of the seminiferous epithelium in the adult testis

2014-12-17 | GSE64214 | GEO

Riding the spermatogenic wave: Profiling gene expression within neonatal germ and Sertoli cells during a synchronized initial wave of spermatogenesis

Project description:WIN 18,446/RA treatment of neonatal mice was used to synchronize the initial wave of spermatogenesis and identify novel messages expressed within either germ or Sertoli cells as spermatogonia enter meiosis.

2014-05-01 | GSE54408 | GEO

Retinoic acid-induced differentiation of porcine spermatogonia in vitro

Project description:Spermatogenesis is an intricate developmental process occurring in testes by which spermatogonial stem cells (SSCs) self-renew and differentiate into mature sperm. The molecular mechanisms for SSC self-renewal and differentiation, while have been well studied in mice, may differ between mice and domestic animals including pigs. To gain knowledge about the molecular mechanisms for porcine SSC self-renewal and differentiation that have to date been poorly understood, here we isolated and enriched primitive spermatogonia from neonatal porcine testes, and exposed the cells to retinoic acid, a direct inducer for spermatogonial differentiation. We then identified that retinoic acid could induce porcine primitive spermatogonial differentiation into leptotene spermatocyte-like cells, which was accompanied by a clear transcriptomic alteration, as revealed by the RNA-sequencing analysis. We also compared retinoic acid-induced in vitro porcine spermatogonial differentiation with the in vivo process, and compared retinoic acid-induced in vitro spermatogonial differentiation between pigs and mice. Furthermore, we analyzed retinoic acid-induced differentially expressed long non-coding RNAs (lncRNAs), and demonstrated that a pig-specific lncRNA, lncRNA-106504875, positively regulated porcine spermatogonial proliferation by targeting the core transcription factor ZBTB16. Taken together, these results would help to elucidate the roles of retinoic acid in porcine spermatogonial differentiation, thereby contributing to further knowledge about the molecular mechanisms underlying porcine SSC development and, in the long run, to optimization of both long-term culture and induced differentiation systems for porcine SSCs.

2023-01-09 | GSE219031 | GEO

10x Genonics Drop-seq single-cell RNA-seq of isolated Adult ID4-EGFP mouse spermatogonia, spermatocytes, spermatids & steady-state spermatogenic cells

Project description:To reveal distinct transcriptomes associated with various spermatogenic cells, including spermatogonial stem cells and all of their subsequent progeny, single-cell transcriptomes from Adult ID4-EGFP+ spermatogonia (sorted for brightest or dimmest), StaPut-enriched spermatocytes and spermatids, or unselected steady-state spermatogenic cells were used for 10x Genomics analysis. The GFP-bright and dim phenotypes exhibit distinct fates when assayed by transplantation, with ID4-EGFPbright cells highly enriched for SSCs, and ID4-EGFPdim cells enriched for progenitors. We used the 10x Genomics Chromium (Drop-Seq) to perform single-cell RNA-seq

2018-11-06 | GSE109033 | GEO

ATAC-seq of mouse spermatogonia cells at two developmental stages (PND15 and adult)

Project description:In mammals, spermatogonial cells are undifferentiated male germ cells in testes that exit quiescence after birth, and self-renew or differentiate to produce spermatogenic cells and functional sperm across life. However, what drives this developmental transition at the transcriptional and chromatin level is still poorly understood. Here we characterized the transcriptome and chromatin accessibility landscape of the genome from spermatogonial cells purified at different stages of postnatal development and in adult.

2023-12-30 | E-MTAB-12722 | biostudies-arrayexpress

Roles of Stra8 and Tcerg1l in retinoic acid induced spermatogonial differentiation in mouse.

Project description:Retinoic acid (RA) induces spermatogonial differentiation, but the mechanism by which it operates remains largely unknown. We developed a germ cell culture assay system to study genes involved in spermatogonial differentiation triggered by RA. Stimulated by Retinoic Acid 8 (Stra8), an RA-inducible gene, is indispensable for meiosis initiation, and its deletion results in a complete block of spermatogenesis at the pre-leptotene/zygotene stage due to failure to complete pre-meiotic DNA replication. To interrogate the role of Stra8 in RA mediated differentiation of spermatogonia, we derived germ cell cultures from the neonatal testis of both wild type and Stra8 knock-out mice. We provide the first evidence that Stra8 plays a crucial role in modulating the responsiveness of undifferentiated spermatogonia to RA and facilitates transition to a differentiated state. Stra8-mediated differentiation is achieved through downregulation of a large portfolio of genes and pathways, most notably including genes involved in the spermatogonial stem cell self-renewal process. We also report here for the first time the role of Transcription Elongation Regulator-1 Like (Tcerg1l) as a downstream effector of RA-induced spermatogonial differentiation.

2021-05-05 | GSE173873 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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