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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Development of FGF2-dependent pluripotent stem cells showing naïve state characteristics from murine preimplantation inner cell mass

ABSTRACT: A unique embryonic stem cells showing naïve state was established from primplantation mouse blastocyst but maintaind their self renew under FGF2 stimulus condition We used microarray to compare gene expression patterns of our pluripotent stem cell line (named FGF-ESC) with ESCs or EpiSCs in addition to inner cell mass from E3.5 preimplantation blastocyst as in vivo control. Total RNA was extracted from FGF-ESC, ESC, EpiSC and inner cell mass from E3.5 preimplantation blastocyst, and served for microarray analysis using Affymetrix Mouse Gene 2.1 Array

ORGANISM(S): Mus musculus

SUBMITTER: Manabu Ozawa

PROVIDER: E-GEOD-53275 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Development of FGF2-dependent pluripotent stem cells showing naïve state characteristics from murine preimplantation inner cell mass

Project description:A unique embryonic stem cells showing naïve state was established from primplantation mouse blastocyst but maintaind their self renew under FGF2 stimulus condition We used microarray to compare gene expression patterns of our pluripotent stem cell line (named FGF-ESC) with ESCs or EpiSCs in addition to inner cell mass from E3.5 preimplantation blastocyst as in vivo control.

2014-05-01 | GSE53275 | GEO

Time-series of gene expression in female murine ES cells during EpiSC differentiation

Project description:Embryonic stem cells (ESC) are derived from the inner cell mass of the blastocyst in the presence of leukemia inhibitory factor (LIF). In vivo these cells then differentiate into epi stem cells (EpiSC) that can be derived from the Epiblast in presence of Fgf2 and ActivinA. In this study, female ESCs cultured in 2i medium have been differentiated into EpiSC for 3.5 days in vitro by addition of Fgf2 and Activin A. The gene expression profile was analyzed every 4-12 h using mouse exon arrays. Mouse Pgk12.1 ES cells were differentiated into EpiSC, samples were taken every 4-12 hours for 84 hours in total

2012-04-10 | E-GEOD-34243 | biostudies-arrayexpress

RNA-seq of mouse embryonic stem cells differentiated to EpiSCs and further to presomitic mesoderm (PSM) via Wnt activation (CHIR99021) to study the influence of FGF signaling on PSM induction

Project description:Presomitic mesoderm (PSM) cells are the precursors of the somites, which flank both sides of the neural tube and give rise to the musculo-skeletal system shaping the vertebrate body. WNT and FGF signalling control the formation of both the PSM and the somites, and show a graded distribution with highest levels in the posterior PSM. We have employed reporter for the PSM control gene Tbx6 to investigate the differentiation of mouse ESCs from the naĂŻve state to PSM state. Feeder-free ESCs were seeded and grown on fibronectin (3-5 ng/ml)-coated plates in ESC medium containing LIF, PD0325901 and CHIR99021 (2i medium) to bring them to a naive state of pluripotency. Following this, the cells were brought to an EpiSC state by treating them with Activin A and FGF2. The EpiSC-like cells were then differentiated to PSM using CHIR99021 either alone or along with FGF ligands, FGF2 or FGF8 (Low concentration: 10 ng/ml or High concentration: 250ng/ml).

2016-06-01 | E-MTAB-3784 | biostudies-arrayexpress

Pramel7-Cul2 axis establishes ground-state gene expression in embryonic stem cells

Project description:Pluripotency is established in E4.5 preimplantation epiblast, the founder populations of the adult embryo. The establishment of in vitro models that closely resemble ground-state pluripotency represents an important opportunity to study early embryo development. Pramel7, a protein highly expressed in the inner cell mass (ICM) but expressed at low levels in embryonic stem cells (ESCs), was implicated in the establishment of ground-state pluripotency. Increasing Pramel7 expression in developmentally advanced ESC+serum causes global DNA hypomethylation and induces a gene expression signature close to developmental ground-state. However, how Pramel7 affects gene expression remains elusive. Here we show that Pramel7 associates and recruits to chromatin Cullin2 (Cul2), a component of Cullin2-RING E3 ubiquitin ligase complex that is implicated in proteasomal degradation of target substrates. Pramel7-Cul2 interaction is required for the establishment of ground-state gene expression signature. We show that Pramel7/Cul2 directly target many components of repressive chromatin, including components of the Nucleosome Remodelling and Deacetylase (NuRD) complex, for degradation. We identified a set of Pramel7-regulated genes that depend on Cul2 and associate with the NuRD component Chd4. The majority of these genes are upregulated in ESCs expressing Pramel7 and linked to pluripotency pathways. Finally, we show that Chd4 binding to these genes is impaired by Pramel7 in a Cul2-dependent manner. Our data link proteasome pathway to the establishment of ground-state gene expression, offering insights that could facilitate the establishment of in vitro models to reproduce the in vivo ground-state pluripotency.

2024-01-08 | PXD032184 | Pride

Bulk and single-cell RNA-seq of mouse blastocyst, blastoid Trophoblast stem cells and Embryonic stem cells

Project description:We did bulk and single cell RNA sequencing of blastocysts, blastoids, trophoblast stem cells (TSC) and embryonic stem cells (ESC). The goal of these experiment is to describe the transformations of the transcriptome occurring within cells (TSC, ESC) upon formation of a blastoid. E3.25 and E3.5 blastocysts are used as controls. To this end, we first did RNA sequencing of intact structures (E3.25 and E3.5 blastocysts, blastoids, and parental cell lines). In a different series of experiments, we micro-dissected blastocyst, blastoid or trophosphere structures into single cells, and sequenced their mRNAs, to infer cell identity and transcriptome variations.

2018-05-07 | GSE99786 | GEO

Stem cell lines of the early mouse embryo

Project description:Expression profiling of stem cell lines derived from the early embryo representing the trophoblast, primitive endoderm, early epiblast (inner cell mass E3.5) and late post-implantation epiblast (E5.5). Cells were grown without feeders and harvested. Comparisons were made to provide evidence of unique gene expression between the cell lines. Specifically, pre-implantation (ICM, epiblast and primitive endoderm, and trophoblast), as well as pre-implantation and post-implantation epiblasts.

2012-05-21 | E-GEOD-34799 | biostudies-arrayexpress

Chromatin remodeling in bovine oocytes and preimplantation embryos

Project description:Profiles of H3K4me3, H3K27ac, H3K27me3 and H3K9me3 in bovine GV oocytes and preimplantation embryos, and the characterization of chromatin accessibility in bovine blastocyst, inner cell mass and trophectoderm.

2023-02-16 | GSE193640 | GEO

Transcription profiling by array of mouse embyronic stem cells and ESD-EpiSCs

Project description:The comparison of mouse ESCs and ESD-EpiSCs was done using three biological replicates for each cell type. ESC samples (ESR1 p10, p20, ESR1/E p15) and ESD-EpiSC samples (EpiSC-7 p20, EpiSC-5 p22, and EpiSC-7 p25) were used for microarray analysis. Total RNA was extracted using Trizol and labeled and hybridized to Agilent Whole Mouse Genome Oligo 4X44K Microarrays (one-color platform) according to the manufacturers protocols.

2010-05-12 | E-MEXP-2691 | biostudies-arrayexpress

Functional roles of the chromatin remodeler SMARCA5(SNF2H) in mouse and bovine preimplantation embryos

Project description:Upon fertilization, extensive chromatin reprogramming occurs during preimplantation development. Growing evidence reveals species-dependent regulations of this process in mammals. ATP-dependent chromatin remodeling factor SMARCA5 (also known as SNF2H) is required for peri-implantation development in mice. However, the specific functional role of SMARCA5 in preimplantation development and if it is conserved among species remain unclear. Herein, comparative analysis of public RNA-seq datasets reveals that SMARCA5 is universally expressed during oocyte maturation and preimplantation development in mice, cattle, humans and pigs with species-specific patterns. Immunostaining analysis further describes the temporal and spatial changes of SMARCA5 in both mouse and bovine models. siRNA-mediated SMARCA5 depletion reduces the developmental capability and compromises the specification and differentiation of inner cell mass in mouse preimplantation embryos. Indeed, OCT4 is not restricted into the inner cell mass and the formation of epiblast and primitive endoderm disturbed with reduced NANOG and SOX17 in SMARCA5-deficient blastocysts. RNA-seq analysis shows SMARCA5 depletion causes limited effects on the transcriptomics at the morula stage, however, dysregulates 402 genes, including genes involved in transcription regulation and cell proliferation at the blastocyst stage in mice. By comparison, SMARCA5 depletion does not affect the development through the blastocyst stage but significantly compromises the blastocyst quality in cattle. Primitive endoderm formation is greatly disrupted with reduced GATA6 in bovine blastocysts. Overall, our studies demonstrate the importance of SMARCA5 in fostering the preimplantation development in mice and cattle while there are species-specific effects.

2021-05-31 | GSE171760 | GEO

Profiling of Y1 cells treated with FGF-2 reveals parallels with oncogene-induced senescence

Project description:Paradoxically, oncogenes that drive cell cycle progression may also trigger pathways leading to senescence, thereby inhibiting the growth of tumorigenic cells. Along these lines, Y1 cells, which carry an amplification of Ras, become senescent after treatment with the mitogen FGF-2. To understand how FGF-2 promotes senescence, we profiled the epigenome, transcriptome, proteome, and phospho-proteome of Y1 cells stimulated with FGF-2. FGF-2 caused delayed acetylation of histone H4 and higher levels of H3K27me3. Sequencing analysis revealed decreased expression of cell cycle-related genes with concomitant loss of H3K27ac. In contrast, FGF-2 promoted the expression of p21, various cytokines, and MAPK-related genes. Nuclear envelope proteins, particularly lamin B1, displayed increased phosphorylation in response to FGF-2. Proteome analysis suggested alterations in cellular metabolism, as evident by modulated expression of enzymes involved in purine biosynthesis, tRNA aminoacylation, and the TCA cycle. Altogether, the response of Y1 cells to FGF-2 is consistent with oncogene-induced senescence. We propose that Y1 cells enter senescence due to deficient cyclin expression and high levels of p21, which may stem from DNA damage or TGFb signaling.

2021-06-16 | PXD020688 | Pride

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