RNA-Seq of human embryonic stem cells over expressing NANOS3 and DAZL
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB10573 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR990405_1.fastq.gz | Fastqsanger.gz | |||
| ERR990405_2.fastq.gz | Fastqsanger.gz | |||
| ERR990406_1.fastq.gz | Fastqsanger.gz | |||
| ERR990406_2.fastq.gz | Fastqsanger.gz | |||
| ERR990407_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 18 |
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Project description:Human embryonic stem cells (cell line HS401) were transfected with piggyBac over expression constructs for germ cell specific RNA binding proteins, Nanos homolog 3 (NANOS3) or Deleted in azoospermia-like (DAZL). Cells transfected with a construct without open reading frame (MOCK), were used as control. Biological triplicates from separate transfections were used for analysis. Total RNAs were ribodepleted and sequenced on one lane on an Illumina HiSeq2500 with a 2x101 setup in HighOutput mode.
2016-10-19 | E-MTAB-3849 | biostudies-arrayexpress
Project description:We developed a method to identify chromatin-associated proteins by mass spectrometry. In addition to many known DNA and chromatin-binders, we identified several RNA-binding proteins in the chromatin composition of mouse embryonic stem cells (mESC). Interestingly, we found Dazl as a RBP that specifically binds to chromatin in mESC grown in 2iL condition. So far, Dazl was reported as a RBP that regulates the stability of transcripts in cytoplasm. To identify the binding sites of Dazl on the genome, we carried out a ChIP-seq experiment. As a result, we detected about 1300 reproducible Dazl ChIP-seq peaks. Interestingly, most of the peaks are located close to the transcription start sites of developmental and pluripotency-related genes.
2020-12-25 | E-MTAB-9302 | biostudies-arrayexpress
Project description:Primary ovarian insufficiency (POI) is a complex disorder that affects many genes and the underlying molecular mechanisms remain to be fully elucidated. In this study, a homozygous point mutation, c.808C>T, in the DAZL gene of a POI patient was identified. This homozygous variant causes a C-terminal truncation of DAZL and down-regulation of germ-line gene NANOS3 expression, among other dysregulated genes, in human primordial germ cells (hPGCs) in vitro. Mechanistically, we discovered that the truncated DAZL had defects in regulating mRNA translation for NANOS3, VASA, and SYCP3 - all essential for gametogenesis. Additionally, the truncated DAZL showed impaired interaction with Poly(A)-binding proteins (PABPs), a crucial component of the translation initiation complex. At the cellular level, the truncated mutation resulted in increased apoptosis of in vitro hPGCs. Our findings reveal that the c.808C>T mutation in DAZL causes dysregulated expressions of many genes, increases germ cell apoptosis and ultimately leads to POI.
2023-10-18 | GSE245155 | GEO
Project description:iCLIP of Dazl in mouse embryonic stem cells
| PRJEB39321 | ENA
Project description:ChIP-Seq of Dazl in mouse embryonic stem cells
| PRJEB39230 | ENA
Project description:In this experiment we would like to identify the binding sites of Dazl on the transcriptome of mESCs. To do that, we carried out an iCLIP experiment using mESCs grown in 2iL condition.
2020-12-25 | E-MTAB-9332 | biostudies-arrayexpress
Project description:The mechanisms underlying human germ cell development are largely unknown, partly due to the scarcity of primordial germ cells and the inaccessibility of the human germline to genetic analysis. Human embryonic stem cells can differentiate to germ cells in vitro and can be genetically modified to study the genetic requirements for germ cell development. Here, we studied NANOS3 and DAZL, which have critical roles in germ cell development in several species, via their over expression in human embryonic stem cells using global transcriptional analysis, in vitro germ cell differentiation, and in vivo germ cell formation assay by xenotransplantation. We found that NANOS3 over expression prolonged pluripotency and delayed differentiation. In addition, we observed a possible connection of NANOS3 with inhibition of apoptosis. For DAZL, our results suggest a post-transcriptional regulation mechanism in hES cells. In addition, we found that DAZL suppressed the translation of OCT4, and affected the transcription of several genes associated with germ cells, cell cycle arrest, and cell migration. Furthermore, DAZL over expressed cells formed spermatogonia-like colonies in a rare instance upon xenotransplantation. These data can be used to further elucidate the role of NANOS3 and DAZL in germ cell development both in vitro and in vivo.
| S-EPMC5074499 | biostudies-literature
Project description:RNA-Seq of human embryonic stem cells over expressing NANOS3 and DAZL
2025-01-23 | E-MTAB-3849 | ExpressionAtlas
Project description:Primordial germ cells (PGCs) are the embryonic precursors to egg and sperm. When removed from the embryonic gonad, PGCs can give rise to embryonic germ cell lines (EGs), pluripotent stem cells that display most of the characteristics of embryonic stem cells (ESCs) including the ability to form teratomas and to contribute to chimera formation. In mice, EG cells can be derived between E8.5 up to E12.5 of embryonic development, at which point the PGCs undergo sexual differentiation and in the male transition into unipotent gonocytes. Dazl, a germ cell-specific RNA-binding protein, is specifically expressed in developing PGCs and is required for proper germ cell development. Dazl knockout mice are infertile, but the molecular mechanisms underlying this phenotype are still unknown. Here we demonstrate that Dazl localizes in granular structures in mammalian PGCs but not in ESCs. We demonstrate Dazl plays a central role in a large mRNA/protein interactive network that includes members of Fragile-X family RNA-binding proteins. We demonstrate that Dazl and Fxr1 play a central role in these granules and directly regulate the translation of specific core pluripotency factors, including Sox2 and Suz12. RNA species interacting specifically with Dazl in juvenile testicular germ cells were identified by RNA-IP microarray analysis. This dataset contains data from native RNA-IPs from P14 Dazl-GFP transgenic mouse testes. Native RNA-IP (anti-V5 and anti-PABP1) experiments from juvenile testicular germ cells expressing Dazl-GFP-V5. Input Total RNA and mock IP with normal mouse IgG were used as controls. Control and IP-enriched RNA samples were analyzed by Agilent Mouse Whole Genome 4X44K one-color microarrays. Two replicates for each condition were done.
2013-12-31 | E-GEOD-39545 | biostudies-arrayexpress
Project description:Primordial germ cells (PGCs) are the embryonic precursors to egg and sperm. When removed from the embryonic gonad, PGCs can give rise to embryonic germ cell lines (EGs), pluripotent stem cells that display most of the characteristics of embryonic stem cells (ESCs) including the ability to form teratomas and to contribute to chimera formation. In mice, EG cells can be derived between E8.5 up to E12.5 of embryonic development, at which point the PGCs undergo sexual differentiation and in the male transition into unipotent gonocytes. Dazl, a germ cell-specific RNA-binding protein, is specifically expressed in developing PGCs and is required for proper germ cell development. Dazl knockout mice are infertile, but the molecular mechanisms underlying this phenotype are still unknown. Here we demonstrate that Dazl localizes in granular structures in mammalian PGCs but not in ESCs. We demonstrate Dazl plays a central role in a large mRNA/protein interactive network that includes members of Fragile-X family RNA-binding proteins. We demonstrate that Dazl and Fxr1 play a central role in these granules and directly regulate the translation of specific core pluripotency factors, including Sox2 and Suz12. RNA species interacting specifically with Dazl in primordial germ cells were identified by RNA-IP microarray analysis. This dataset contains data from native RNA-IPs without UV-crosslinking. Two independent native RNA-IP (anti-V5 and anti-GFP) experiments from in vitro derived primordial germ cells expressing Dazl-GFP-V5. Input Total RNA and mock IP using normal mouse IgG were used as controls. Control and IP-enriched RNA samples were analyzed by Agilent Mouse Whole Genome 4X44K one-color microarrays.
2013-12-31 | E-GEOD-39544 | biostudies-arrayexpress