Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

An Intermediate Pluripotent State Controlled by microRNAs is Required for the Naïve to Primed Stem Cell Transition

ABSTRACT: An Intermediate Pluripotent State Controlled by microRNAs is Required for the Naïve to Primed Stem Cell Transition

PROVIDER: PRJNA445698 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR6898240.fastq.gz	Fastqsanger.gz
	SRR6898250.fastq.gz	Fastqsanger.gz
	SRR6898260.fastq.gz	Fastqsanger.gz
	SRR6898270.fastq.gz	Fastqsanger.gz
	SRR6898241.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 42

Similar Datasets

An Intermediate Pluripotent State Controlled by microRNAs is Required for the Naïve to Primed Stem Cell Transition

Project description:The embryonic stem cell (ESC) transition from naive to primed pluripotency is marked by major changes in cellular properties and developmental potential. ISY1 is implicated in miRNA biogenesis yet its widespread role and relevance to ESC biology remain unknown. Here we find that highly dynamic ISY1 expression during the naïve to primed ESC transition defines a unique phase of ‘poised’ pluripotency characterized by distinct miRNA and mRNA transcriptomes and widespread poised cell contribution to mouse chimeras. Loss- and gain-of-function experiments reveal that ISY1 promotes exit from the naïve state, is necessary and sufficient to induce and maintain poised pluripotency, and that persistent ISY1 overexpression inhibits the transition from the naïve to the primed state. We identify a large subset of ISY1-dependent miRNAs that can rescue the inability of miRNA-deficient ESCs to establish the poised state and transition to the primed state. Thus, dynamic ISY1 regulates poised pluripotency through miRNAs to control ESC fate.

2018-03-29 | GSE112334 | GEO

Comprehensive miRNA profiling of human naïve, intermediate and primed pluripotent stem cells

Project description:Comprehensive miRNA profiling of human naïve, intermediate and primed pluripotent stem cells

| PRJNA526900 | ENA

Comprehensive miRNA profiling of human naïve, intermediate and primed pluripotent stem cells

Project description:Naïve human pluripotent stem cells (hPSC) represent an earlier time-point in embryogenesis than conventional, ‘primed’ hPSCs. We present a comprehensive miRNA profiling of naïve-to-primed transition in hPSC, a process resembling aspects of early in vivo embryogenesis. We identify miR-143-3p and miR-22-3p as markers of the naïve state and miR-363-5p, several members of the miR-17 family, miR-302 family as primed markers. We uncover that miR-371-373 are highly upregulated in naïve hPSC. MiR-371-373 are the human homologs of the mouse miR-290 family, which are the most highly expressed miRNAs in mPSC. This aligns with the consensus that naïve hPSC resemble mPSC, showing that the absence of miR-371-373 in conventional hPSC is due to cell state rather than a species difference.

2020-06-29 | GSE128260 | GEO

Transcriptional analysis of intermediates during human primed and naïve reprogramming.

Project description:We report transcriptional time-course profiling (RNA-seq) of intermediate populations of reprogramming of human fibroblasts into primed and naïve pluripotent states

2020-05-15 | GSE149694 | GEO

Chromatin accessibility analysis of intermediates during human primed and naïve reprogramming.

Project description:We report chromatin accessibility time-course profiling (ATAC-seq) of intermediate populations of reprogramming of human fibroblasts into primed and naïve pluripotent states

2020-05-15 | GSE147641 | GEO

Single-nucleus RNA sequencing of intermediates during human primed and naïve reprogramming.

Project description:We report single-nucleus RNA time-course profiling of intermediate populations of reprogramming of human fibroblasts into primed and naïve pluripotent states

2020-05-15 | GSE147564 | GEO

Single Cell Sequencing Reveals Early PGC-like Intermediates During Mouse Primed to Naïve Transition

Project description:Single cell analysis provides clarity unattainable with bulk approaches. Here we apply single cell RNA-seq to a newly established BMP4 induced mouse primed to naive transition (Bi-PNT) system and show that the reset is not a direct reversal of cell fate but through developmental intermediates. We first show that mEpiSCs bifurcate into c-Kit+ naïve and c-Kit- placenta-like cells, among which, the naive branch undergoes further transition through a primordial germ cell-like cells (PGCLCs) intermediate capable of spermatogenesis in vivo. Indeed, deficiency of Prdm1/Blimp1, the key regulator for PGC specification, blocks the induction of PGCLCs and naïve cells. Instead, Gata2 knockout arrests placenta-like fate, but facilitates the generation of PGCLCs. Our results not only reveal a newly cell fate dynamics between primed and naive states at single-cell resolution, but also provide a model system to explore mechanisms involved in regaining germline competence from primed pluripotency.

2021-03-09 | GSE147088 | GEO

Reorganization of enhancer patterns in transition from naïve to primed pluripotency (RNA-seq)

Project description:Naïve and primed pluripotency is characterized by distinct signaling requirements, transcriptomes and developmental properties, but both cellular states share key transcriptional regulators, Oct4, Sox2 and Nanog. Here we demonstrate that transition between these two pluripotent states is associated with widespread Oct4 relocalization, mirrored by global rearrangement of enhancer chromatin landscapes. Our genomic and biochemical analyses identified candidate mediators of primed state-specific Oct4 binding, including Otx2 and Zic2/3. Even in the absence of other differentiation cues, premature Otx2 overexpression is sufficient to exit the naïve state, induce transcription of a large subset of primed pluripotency-associated genes and redirect Oct4 to thousands of previously inaccessible sites. However, ability of Otx2 to engage new enhancer regions is determined by its levels, cis-encoded properties of the sites and signaling environment. Our results illuminate regulatory mechanisms underlying pluripotency and suggest that capacity of transcription factors such as Otx2 and Oct4 to function as pioneers is highly context-dependent transcription profile of ESCs and EpiLCs to analzye changes during differentiation and the effect of Otx2 loss and overexpression on the differentiation properties

2014-06-05 | E-GEOD-56096 | biostudies-arrayexpress

Single-cell RNA sequencing of intermediates during human primed and naïve reprogramming.

Project description:We report single-cell RNA time-course profiling of intermediate populations of reprogramming of human fibroblasts into primed and naïve t2iLGoY and RSeT pluripotent states

2020-05-15 | GSE150311 | GEO

Translational and Post-translational LC-MS of Naïve and Primed hESCs

Project description:Deciphering the regulatory network for human naïve and primed pluripotency is of fundamental theoretical and applicable significance. Here, by combining quantitative proteomics, phosphoproteomics and acetylproteomics analyses, we revealed RNA processing and translation as the most differentially-regulated processes between naïve and primed human embryonic stem cells (hESCs). While glycolytic primed hESCs rely predominantly on eIF4E-mediated cap-dependent pathway for protein translation, naïve hESCs with reduced mTORC1 activity are more tolerant to blockage of eIF4E-dependent translation, and their bivalent metabolism allows for translating selective mRNAs via both eIF4E-dependent and eIF4E-independent/eIF4A2-dependent pathways to form a more compact naïve proteome. Globally up-regulated proteostasis system and down-regulated post-translational modification system help to further refine and maintain the naïve proteome that is compatible with the more rapid cycling of naïve hESCs, where CDK1 plays an indispensable coordinative role.

2021-12-10 | PXD030230 | Pride

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