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RNA-seq of wild-type mouse embryonic stem cells (mESC) during spontaneous differentiation

ABSTRACT: RNA-seq of wild-type mouse embryonic stem cells (mESC) during spontaneous differentiation

PROVIDER: PRJEB38938 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR4265400_1.fastq.gz	Fastqsanger.gz
	ERR4265400_2.fastq.gz	Fastqsanger.gz
	ERR4265401_1.fastq.gz	Fastqsanger.gz
	ERR4265401_2.fastq.gz	Fastqsanger.gz
	ERR4265402_1.fastq.gz	Fastqsanger.gz

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RNA-seq of wild-type mouse embryonic stem cells (mESC) during spontaneous differentiation

Project description:Transcriptomic analysis of mouse embryonic stem cells (mESC) maintained in the pluripotent state or allowed to differentiate for 3 or 7 days by leukaemia inhibitory factor (LIF) withdrawal.

2023-05-27 | E-MTAB-9261 | biostudies-arrayexpress

Murine embryonic stem cells synthesize retinoic acid to promote their own spontaneous differentiation

Project description:Embryonic stem cells (ESC) are derived from blastocyst-stage embryos and are thought to be functionally equivalent to the inner cell mass in their developmental potential. ESCs pluripotency is maintained through a complex interplay of different signaling pathways and a network of transcription factors, which is centered around Oct3/4, Sox2 and Nanog. Although, in general, much is known about this pluripotency self-renewal circuitry, the molecular events that lead ESC to exit from pluripotency and begin differentiation are currently less known. Retinoic acid, an active metabolite of the vitamin A (retinol), plays important and pleiotropic roles in vertebrate embryonic development and ESC differentiation. Here we demonstrate that RA promotes early steps of ESC differentiation, and that ESC increase their capacity to synthesize RA during spontaneous differentiation as embryoid bodies, up-regulating the RA biosynthetic pathway components RDH1, RDH10, ADH3, RALDH2, and CRABP2. Microarray derived from total RNA of mESC not treated or treated with all-trans retinoic acid (ATRA) for 2 hours.

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Canonical Wnt pathway controls mESCs self-renewal through inhibition of spontaneous differentiation via β-catenin/TCF/LEF functions

Project description:The Wnt/β-catenin signalling pathway is a key regulator of embryonic stem cell self-renewal and differentiation. Constitutive activation of this pathway has been shown to significantly increase mouse embryonic stem cell (mESC) self-renewal and pluripotency marker expression. In this study, we generated a novel β-catenin knock-out model in mESCs by using CRISPR/Cas9 technology to delete putatively functional N-terminally truncated isoforms observed in previous knock-out models. While we showed that aberrant N-terminally truncated isoforms are not functional in mESCS, we observed that canonical Wnt signalling is not active in mESCs, as β-catenin ablation does not alter mESC transcriptional profile in LIF-enriched culture conditions; on the other hand, Wnt signalling activation represses mESC spontaneous differentiation. We also showed that transcriptionally silent β-catenin (ΔC) isoforms can rescue β-catenin knock-out self-renewal defects in mESCs, cooperating with TCF1 and LEF1 in the inhibition of mESC spontaneous differentiation in a Gsk3 dependent manner.

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SIRT1 deficiency enhances RA induced mESC differentiation

2014-08-21 | GSE59140 | GEO

SIRT1 deficiency enhances RA induced mESC differentiation

Project description:Retinoid homeostasis is critical for normal embryonic development, and both the deficiency and excess of these compounds are associated with congenital malformations. Here we found that SIRT1, the most conserved mammalian NAD+-dependent deacetylase, contributes to the maintenance of homeostatic retinoic acid (RA) signaling and modulates mouse embryonic stem cell (mESC) differentiation. Our data show that SIRT1 deficiency enhances RA signaling, thereby accelerating mES cell differentiation in response to RA. Our findings highlight the importance of SIRT1 in transcriptional regulation of ESC pluripotency and embryogenesis. Three pairs of sh-Control and sh-SIRT1 E14 mESC cells (with dulpicate for each sample) were treated with vehicle ethanol or with 20 nM of RA for 2 days. Total RNA was isolated using a Qiagen RNA easy mini kit with on-column DNAseI treatment. RNA quality was validated with the Agilent 2100 Bioanalyzer in the microarray facility. Three-pairs of ethanol treated samples, and 4 RA treated sh-Control, and 6 RA treated sh-SIRT1 samples were analyzed by Agilent Whole Mouse Genome 4x44 formate oligo arrays (014868) (Agilent Technologies) following the Agilent 1-color microarray-based gene expression analysis protocol.

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Murine embryonic stem cells synthesize retinoic acid to promote their own spontaneous differentiation

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Integrity of the short arm of nuclear pore Y-complex is required for mouse embryonic stem cell growth and differentiation

Project description:Nuclear pore complexes (NPCs) are established players in cell division and differentiation. However studies on the contribution of individual NPC subunits to these processes are still scarce. Here we have used mouse embryonic stem cells (mESCs) to characterize the role of structural components of the NPCs, focusing on the short arm of the Y-complex that comprises Nup85, Seh1 and Nup43. We show that Seh1 and Nup43, although dispensable at the pluripotent stage, are required for normal cell growth rates at that stage and for mESC viability upon differentiation. Lack of Seh1 or Nup43 in mESCs is associated with a mild reduction of NPC density that is also observed when Seh1 interaction with Nup85 is impaired. Nevertheless, mESC proliferation and differentiation are not altered in these ∆E2-GFP-Nup85 mutants, indicating that it is the integrity of the Y-complex, rather than the number of NPCs, that is critical to ensure these processes.

2021-05-20 | PXD022190 | Pride

circular RNA Kat6b-e2 expression safeguards self-renewal and lineage differentiation of mouse embryonic stem cells

Project description:Circular RNA has been reported to be dynamically expressed during embryonic development and regulates human embryonic stem cells (hESCs), but the identification and regulation of functional circular RNA in mouse embryonic stem cells (mESC) remains unclear. Here we found over 1,000 circular RNAs in different mESC states. One of these, circular RNA Kat6b-exon2 (circKat6b-e2), was significantly overexpressed in mESCs. Furthermore, short-hair RNA (shRNA) mediated knockdown of circKat6b-e2 expression significantly inhibited mESC self-renewal and EB differentiation. The transcriptome also revealed that circKat6b-e2 is required to ensure the differentiation of the mESC lineage. Finally, we also found that more Alu elements surrounding circKat6b-e2 were necessary factors for its expression. Conclusions: our study shows that Alu element-dependent expression of circKat6b-e2 mediates mESC self-renewal and lineage differentiation.

2022-08-28 | GSE211667 | GEO

Embryonic stem sell differentiation time course

Project description:During in vitro differentiation, pluripotent stem cells undergo extensive remodeling of their gene expression profiles. While studied extensively at the transcriptome level, much less is known about protein dynamics, which might differ significantly from their mRNA counterparts. Here, we present deep proteome-wide measurements of protein levels during the differentiation of embryonic stem cells.

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Mouse embryoid body differentiation of wild-type embryonic stem cells

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