RNA sequencing of Epiblast stem cells, nodal inhibited epiblast stem cells and embryonic samples
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE92634 | GEO | 2018/05/29
REPOSITORIES: GEO
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Project description:We reported H3K4me3, H3K27ac and H3K27me3 histone modification in EpiSCs and Nodal inhibited EpiSCs(EpiSCS/F). Using ChIP sequencing, we demonstrate that the active modification of H3K4me3 and H3K27ac level are higher in EpiSCS/F, suggesting EpiSCsS/F were in an active chromatin state. Interestingly, H3K27me3, the supressive modification enriched more in EpiSCS/F down regulated genes, suggesting H3K27me3 plays pivital roles in regulating gene expression.
2018-05-29 | GSE92633 | GEO
Project description:Epiblast stem cells (EpiSCs) were derived from the epiblast or the ectoderm (epi/ect) of pre-gastrula stage to late-bud stage mouse embryos. To identify if the EpiSCs retain any original stage specific characteristics or which developmental stage of epi/ect they most closely related to, we performed microarray analysis to compare the gene expression profile of multiple EpiSC lines with that of epi/ect of 7 different stages.
2013-09-15 | GSE46227 | GEO
Project description:Epiblast stem cells (EpiSCs) were derived from the epiblast or the ectoderm (epi/ect) of pre-gastrula stage to late-bud stage mouse embryos. To identify if the EpiSCs retain any original stage specific characteristics or which developmental stage of epi/ect they most closely related to, we performed microarray analysis to compare the gene expression profile of multiple EpiSC lines with that of epi/ect of 7 different stages. Eighteen EpiSC lines established from R1-129 embryos of different stages and 1 line (EpiSC9) imported were harvested in triplicate cultured separately for 3 days. The * marks the subline thawed at a different time and harvested but originated from the same embryo. EpiSC9_T is an RNA sample provided by Dr Tesar. ESCs, iPSCs and MEFs were prepared accordingly. For the epiblast samples, in order to avoid the averaging effect by pooling samples, we linearly amplified the RNA starting from a single epiblast or ectoderm.
2013-09-15 | E-GEOD-46227 | biostudies-arrayexpress
Project description:Pluripotent stem cells provide a platform to interrogate control elements that function to generate all cell types of the body. Despite their utility for modeling development and disease, the relationship of mouse and human pluripotent stem cell states to one another remains largely undefined. We have shown that mouse embryonic stem (ES) cells and epiblast stem cells (EpiSCs) are distinct, pluripotent states isolated from pre- and post-implantation embryos respectively. Human ES cells are different than mouse ES cells and share defining features with EpiSCs, yet are derived from pre-implantation human embryos. Here we show that EpiSCs can be routinely derived from pre-implantation mouse embryos. The pre-implantation-derived EpiSCs exhibit molecular features and functional properties consistent with bona fide EpiSCs. These results provide a simple method for isolating EpiSCs and offer direct insight into the intrinsic and extrinsic mechanisms that regulate the acquisition of distinct pluripotent states. 6 total samples were analyzed. Three pluripotent cell types (mES cells, E3.5 EpiSCs, and E5.5 EpiSCs) were compared with and without treatment of SB431542 for 4 days.
2011-01-25 | E-GEOD-26814 | biostudies-arrayexpress
Project description:Embryonic Stem Cells (ESCs) and Epiblast Stem Cells (EpiSCs) are the in vitro representants of naïve and primed pluripotency, respectively. It is currently unclear how their epigenome underpin the phenotypic and molecular characteristics of these states of pluripotency. Here, we performed the first qualitative and quantitative comparison of DNA methylation between ESCs and EpiSCs. The global level and genomic distribution of DNA methylation were very similar between the two cell types. However, the analysis of promoter methylation patterns in EpiSCs revealed several distinct features: (i) the repression of germline-related genes by DNA methylation, a process already ongoing in ESCs but far more pronounced in EpiSCs; (ii) the hypermethylation of promoters (especially CpG rich) in EpiSC compared to both ESCs and dissected epiblasts from E6.5 and E7.5 embryos; (iii) the inability of hypomethylated (Dnmt-deficient) ESCs to be converted into EpiSCs despite their ability to self-renew. Altogether, our data show that DNA methylation is an important epigenetic regulator of gene expression in EpiSCs and suggest that it is essential for the obtention of EpiSCs.
2014-04-28 | GSE47793 | GEO
Project description:Embryonic Stem Cells (ESCs) and Epiblast Stem Cells (EpiSCs) are the in vitro representants of naM-CM-/ve and primed pluripotency, respectively. It is currently unclear how their epigenome underpin the phenotypic and molecular characteristics of these states of pluripotency. Here, we performed the first qualitative and quantitative comparison of DNA methylation between ESCs and EpiSCs. The global level and genomic distribution of DNA methylation were very similar between the two cell types. However, the analysis of promoter methylation patterns in EpiSCs revealed several distinct features: (i) the repression of germline-related genes by DNA methylation, a process already ongoing in ESCs but far more pronounced in EpiSCs; (ii) the hypermethylation of promoters (especially CpG rich) in EpiSC compared to both ESCs and dissected epiblasts from E6.5 and E7.5 embryos; (iii) the inability of hypomethylated (Dnmt-deficient) ESCs to be converted into EpiSCs despite their ability to self-renew. Altogether, our data show that DNA methylation is an important epigenetic regulator of gene expression in EpiSCs and suggest that it is essential for the obtention of EpiSCs. MethylCap-Seq (DNA methylation profiling) and RNA-Seq of 3 EpiStem Cells (EpiSCs) and 1 Embryonic Stem Cell line of which the data has been submitted to GEO before (part of GEO SuperSeries GSE23943 and GSE31343)
2014-04-28 | E-GEOD-47793 | biostudies-arrayexpress
Project description:To characterize molecular features of new EpiSC lines established by the Wnt inhibition method, global gene expression profiles of the EpiSC lines were determined by microarray, and compared to those of EpiSC lines established by other group using the conventional method. Epiblasts, the source of the EpiSCs, and mESCs were also analyzed. EpiSCs and mESC were maintained as undifferentiated state on feeder layers. The stem cells were then separated from feeders, and RNAs were extracted from the stem cell lines. Embryonic tissues were manually dissected out from mouse embryos of E5.5, E6.5 or E7.5, from which RNAs were extracted.
2014-08-01 | E-GEOD-58735 | biostudies-arrayexpress
Project description:Recently, (in vitro) pluripotent EpiSCs were derived from the post-implantation egg cylinder stage epiblasts of mouse and rat. These EpiSCs resemble and correspond very closely to the conventional human embryonic stem cells (hESCs) in the colony morphology and culture/signaling requirements for maintaining pluripotency, but exhibit a range of significant phenotypic and signaling response differences from the conventional mouse ES cells (mESCs). These observations strongly support the notion that EpiSCs and hESCs are intrinsically similar, and raise an attractive hypothesis: as mESCs and EpiSCs/hESCs represent two distinct pluripotency states: the mESC-like state representing the ICM of pre-implantation blastcyst and the EpiSC-like state representing the post-implantation epiblasts, whether the epiblast state (including conventional hESCs) can be converted back to the ICM state. Despite studies providing evidence that epiblast-like cells exist and transition back and forth within colony of conventional mESCs; mESCs and EpiSCs share substantial set of pluripotency transcriptional factors, including Oct4, Sox2 and Nanog; and mESCs are more stable in culture, in the present study we found that EpiSCs differentiated rapidly under mESC culture conditions and no “spontaneously” converted mESC could be readily identified and isolated over serial passages at the population or clonal level. Remarkably, we found that blockage of the TGFβ pathway or inhibition of the H3K4 demethylase LSD1 with small molecule inhibitors induced dramatic morphological changes of EpiSCs towards mESC phenotypes with activation of some ICM-specific gene expression. However, full conversion of EpiSCs to a mESC-like state with competence to chimeric contribution can only be readily generated with a combination of inhibitors of LSD1 and ALK. These observations underscore a powerful and direct induction of reprogramming from the developmentally later-stage EpiSCs to a mESC-like stage by a synergy of signaling and direct epigenetic modulations. It also highlights a significant role for TGFβ pathway inhibition in promoting reprogramming to and sustaining true pluripotency, which further supports our recent studies in generating chimerism-competent rat pluripotent cells. Collectively, our studies provide a proof-of-concept demonstration that pluripotency-restricted EpiSCs can be readily converted to a mESC-like state in the absence of any genetic manipulation by precise pharmacological control of signaling pathways that distinguish the two pluripotency states and an epigenetic target simultaneously, and offer a convenient experimental system to further study the mechanism. Such method and concept may also provide an avenue for generating a new type of mESC-like human pluripotent cell.
2010-10-30 | GSE17664 | GEO
Project description:Recently, (in vitro) pluripotent EpiSCs were derived from the post-implantation egg cylinder stage epiblasts of mouse and rat. These EpiSCs resemble and correspond very closely to the conventional human embryonic stem cells (hESCs) in the colony morphology and culture/signaling requirements for maintaining pluripotency, but exhibit a range of significant phenotypic and signaling response differences from the conventional mouse ES cells (mESCs). These observations strongly support the notion that EpiSCs and hESCs are intrinsically similar, and raise an attractive hypothesis: as mESCs and EpiSCs/hESCs represent two distinct pluripotency states: the mESC-like state representing the ICM of pre-implantation blastcyst and the EpiSC-like state representing the post-implantation epiblasts, whether the epiblast state (including conventional hESCs) can be converted back to the ICM state. Despite studies providing evidence that epiblast-like cells exist and transition back and forth within colony of conventional mESCs; mESCs and EpiSCs share substantial set of pluripotency transcriptional factors, including Oct4, Sox2 and Nanog; and mESCs are more stable in culture, in the present study we found that EpiSCs differentiated rapidly under mESC culture conditions and no âspontaneouslyâ converted mESC could be readily identified and isolated over serial passages at the population or clonal level. Remarkably, we found that blockage of the TGFβ pathway or inhibition of the H3K4 demethylase LSD1 with small molecule inhibitors induced dramatic morphological changes of EpiSCs towards mESC phenotypes with activation of some ICM-specific gene expression. However, full conversion of EpiSCs to a mESC-like state with competence to chimeric contribution can only be readily generated with a combination of inhibitors of LSD1 and ALK. These observations underscore a powerful and direct induction of reprogramming from the developmentally later-stage EpiSCs to a mESC-like stage by a synergy of signaling and direct epigenetic modulations. It also highlights a significant role for TGFβ pathway inhibition in promoting reprogramming to and sustaining true pluripotency, which further supports our recent studies in generating chimerism-competent rat pluripotent cells. Collectively, our studies provide a proof-of-concept demonstration that pluripotency-restricted EpiSCs can be readily converted to a mESC-like state in the absence of any genetic manipulation by precise pharmacological control of signaling pathways that distinguish the two pluripotency states and an epigenetic target simultaneously, and offer a convenient experimental system to further study the mechanism. Such method and concept may also provide an avenue for generating a new type of mESC-like human pluripotent cell. Global gene-expression analyses of the parnate/mAMFGi cells
2010-10-30 | E-GEOD-17664 | biostudies-arrayexpress
Project description:To characterize the EpiSCs (Epiblast stem cells) we established in our lab, we have employed whole genome microarray expression profiling as a platform to distinguish the EpiSCs (primed state) from ES cells (naïve state).
2018-11-30 | GSE75660 | GEO