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Time course transcriptome capturing a directed extraembryonic endoderm (XEN) differentiation protocol of wild type and Ago2_KO mESCs

ABSTRACT: Time course transcriptome capturing a directed extraembryonic endoderm (XEN) differentiation protocol of wild type and Ago2_KO mESCs

PROVIDER: PRJNA514450 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8434460_1.fastq.gz	Fastqsanger.gz
	SRR8434460_2.fastq.gz	Fastqsanger.gz
	SRR8434470_1.fastq.gz	Fastqsanger.gz
	SRR8434470_2.fastq.gz	Fastqsanger.gz
	SRR8434480_1.fastq.gz	Fastqsanger.gz

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Time course transcriptome capturing a directed extraembryonic endoderm (XEN) differentiation protocol of wild type and Ago2_KO mESCs

Project description:Purpose: The goals of this study was to identify novel regulators of XEN differentiation and the role of AGO2 and miRNAs therein

2022-01-10 | GSE124955 | GEO

BMP4 signalling directs primitive endoderm-derived XEN cells to an extraembryonic visceral endoderm identity

Project description:The visceral endoderm (VE) is an epithelial tissue in the early postimplantation mouse embryo that encapsulates the pluripotent epiblast distally and the extraembryonic ectoderm proximally. In addition to facilitating nutrient exchange before the establishment of a circulation, the VE is critical for patterning the epiblast. Since VE is derived from the primitive endoderm (PrE) of the blastocyst, and PrE-derived eXtraembryonic ENdoderm (XEN) cells can be propagated in vitro, XEN cells should provide an important tool for identifying factors that direct VE differentiation. In this study, we demonstrated that BMP4 signalling induces the formation of a polarized epithelium in XEN cells. This morphological transition was reversible, and was associated with the acquisition of a molecular signature comparable to extraembryonic (ex) VE. Resembling exVE which will form the endoderm of the visceral yolk sac, BMP4-treated XEN cells regulated hematopoiesis by stimulating the expansion of primitive erythroid progenitors. We also observed that LIF exerted an antagonistic effect on BMP4-induced XEN cell differentiation, thereby impacting the extrinsic conditions used for the isolation and maintenance of XEN cells in an undifferentiated state. Taken together, our data suggest that XEN cells can be differentiated towards an exVE identity upon BMP4 stimulation, and therefore represent a valuable tool for investigating PrE lineage differentiation. Total RNA isolated in triplicate from XEN stem cell cultures that were untreated (samples 1-3) or treated with BMP4 growth factor (samples 4-6). Total RNA isolated in triplicate from XEN stem cells that were treated with BMP4 and were flow sorted as Afp::GFP-positive (samples 7-9) or Afp::GFP-negative (samples 10-12).

2011-09-13 | E-GEOD-32094 | biostudies-arrayexpress

BMP and Activin treatment of mouse extraembryonic endoderm (XEN) cells

Project description:XEN cells are derived from the primitive endoderm of mouse blastocysts. In culture and in chimeras they exhibit properties of parietal endoderm. However, BMP signaling promotes XEN cells to form an epithelium and differentiate into visceral endoderm (VE). Of the several different subtypes of VE described, BMP induces a subtype that is most similar to the VE adjacent to the trophoblast-derived extraembryonic ectoderm. The experiment was performed to gain insight into genes regulated by BMP and activin in XEN cells, and also to more precisely define the VE subtypes formed in culture. IM8A1 XEN cells were treated for 6 days with BMP2 (20 ng/ml, R&D Systems), activin A (30 ng/ml, Peprotech), both, or neither in GMEM + 10% fetal bovine serum.

2011-11-10 | E-GEOD-32199 | biostudies-arrayexpress

BMP4 signalling directs primitive endoderm-derived XEN cells to an extraembryonic visceral endoderm identity

2011-09-14 | GSE32094 | GEO

BMP and Activin treatment of mouse extraembryonic endoderm (XEN) cells

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OCT4 is expressed in extraembryonic endoderm stem (XEN) cell progenitors during somatic cell reprogramming

Project description:During development, progenitors of embryonic stem (ES) and extraembryonic endoderm stem (XEN) cells are concomitantly specified within the inner cell mass (ICM) of the mouse blastocyst. Similarly, XEN cells are induced (iXEN cells) alongside induced pluripotent stem (iPS) cells following overexpression ofOct4,Sox2,Klf4andMyc(OSKM) during somatic cell reprogramming. It is unclear how or why this cocktail produces both stem cell types, but OCT4 has been associated with non-pluripotent outcomes. In this report, we show that, during OSKM reprogramming, many individualOct4-GFP-expressing cells are fated to become iXEN cells. Interestingly, SKM alone was also sufficient to induce iXEN cell formation, likely via activation of endogenousOct4.These observations indicate that iXEN cell formation is not strictly an artifact ofOct4overexpression. Moreover, our results suggest that a pathway to XEN may be an integral feature of establishing pluripotency during reprogramming, as in early embryo development.

2024-02-15 | GSE244818 | GEO

OSKM induce extraembryonic endoderm stem (iXEN) cells in parallel to iPS cells

Project description:While the reprogramming factors OCT4, SOX2, KLF4, and MYC (OSKM) can reactivate the pluripotency network in terminally differentiated cells, they also regulate expression of non-pluripotency genes in other contexts, such as the mouse primitive endoderm. The primitive endoderm is an extraembryonic lineage established alongside the pluripotent epiblast in the blastocyst, and is the progenitor pool for extraembryonic endoderm stem (XEN) cells. Several studies have shown that endodermal genes are upregulated in fibroblasts undergoing reprogramming, although whether endodermal genes promote or inhibit acquisition of pluripotency is unclear. We show that, in fibroblasts undergoing conventional reprogramming, OSKM-induced expression of endodermal genes leads to formation of induced XEN (iXEN) cells, which possess key properties of blastocyst-derived XEN cells, including morphology, transcription profile, self-renewal, and multipotency. Our data show that iXEN cells arise in parallel to iPS cells, indicating that OSKM are sufficient to drive cells to two distinct fates during reprogramming. Sequence-based mRNA transcriptional profiling of three different cell lines (MEF, XEN, iXEN) with multiple biological replicates, under two different growth medium conditions (ESC medium, XEN medium) for XEN and iXEN cells.

2016-03-03 | E-GEOD-77550 | biostudies-arrayexpress

Transcriptomics of trophoblast stem cells and extraembryonic endoderm stem cells

Project description:To identify splicing regulators with unique regulation in placenta and the trophectoderm lineage, we sequenced trophoblast stem (TS) and Extraembryonic endoderm stem (XEN) cells.

2022-07-01 | GSE181334 | GEO

Derivation of Porcine Extraembryonic Endoderm-like Cells from from Blastocysts

Project description:Extraembryonic endoderm stem (XEN) cells are isolated from PrE (primitive endoderm) of blastocysts. We directly obtained cell lines with XEN characteristics from porcine embryos for the first time. the RNA-seq data indicated highly reproducible gene expression patterns among piPSCs or pXEN-like cell.the gene expression patterns of pXEN-like cells were significantly different from those of piPSCs

2019-11-15 | GSE140414 | GEO

Transcriptome of Ago2_KO mouse embryonic stem cells (mESCs) before and after XEN differentiation

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study was to obtain the trasncriptome of Ago2_KO mESCs to compare it with the transcriptome of WT mESCs before and after XEN conversion (deposit separately).

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