Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA349149 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Human embryonic stem cells do not change their X-inactivation status during differentiation
| PRJNA349145 | ENA
Project description:Human embryonic stem cells do not change their X-inactivation status during differentiation [RNA-Seq]
| PRJNA349151 | ENA
Project description:To investigate the interplay of X-chromosome status and meiosis during primordial germ cell (PGC) maturation, we differentiated mouse embryonic stem cells (ESCs) via epiblast-like cells (EpiLCs) into primordial germ cell like cells (PGCLCs) and further into meiotic germ cells. During the differentiation of PGCLCs, we assessed the kinetics of X-chromosome inactivation and reactivation. We generated allele-specific total RNA-seq datasets to assess gene inactivation and reactivation dynamics, as well as allele-specific single-cell RNA-seq using SMART-Seq v5 to investigate the interplay of meiosis and X-chromosome status in germ cells.
2022-04-04 | GSE169201 | GEO
Project description:Metabolism is vital to cellular function and tissue homeostasis during human lung development. In utero, embryonic pluripotent stem cells undergo endodermal differentiation towards a lung progenitor cell fate that can be mimicked in vitro using induced human pluripotent stem cells (hiPSCs) to study genetic mutations. To identify differences between wild type and surfactant protein B (SFTPB)-deficient cell lines during endoderm specification towards lung, we used an untargeted metabolomics approach to evaluate the developmental changes in metabolites. We found that the metabolites most enriched during the differentiation from pluripotent stem cell to lung progenitor cell, regardless of cell line, were sphingomyelins and phosphatidylcholines, two important lipid classes in fetal lung development. The SFTPB mutation had no metabolic impact on early endodermal lung development. The identified metabolite signatures during lung progenitor cell differentiation may be utilized as biomarkers for normal embryonic lung development.
2021-06-29 | ST002055 | MetabolomicsWorkbench
Project description:We performed an integrated analysis of RNA and proteins at the transition between naïve ES cells and cells primed to differentiate. During this transition, mRNAs coding for chromatin regulators were specifically released from translational inhibition mediated by RNA-Induced Silencing Complex (RISC). This suggests that, prior to differentiation, the propensity of ES cells to change their epigenetic status is hampered by RNA interference. The expression of these chromatin regulators was reinstated following acute inactivation of RISC, and it correlated with loss of stemness markers and activation of early cell differentiation markers in treated ES cells. Comparison between EpiSC derived directly from mouse embryonic stem cells and from Epiblast-Like Aggregates
2016-03-29 | E-GEOD-79650 | biostudies-arrayexpress
Project description:We performed an integrated analysis of RNA and proteins at the transition between naïve ES cells and cells primed to differentiate. During this transition, mRNAs coding for chromatin regulators were specifically released from translational inhibition mediated by RNA-Induced Silencing Complex (RISC). This suggests that, prior to differentiation, the propensity of ES cells to change their epigenetic status is hampered by RNA interference. The expression of these chromatin regulators was reinstated following acute inactivation of RISC, and it correlated with loss of stemness markers and activation of early cell differentiation markers in treated ES cells. Cytoplasmic RNA-protein complexes from mouse embryonic stem cells at different stages of neural in vitro differentiation were immunoprecipitated with anti-Argonaute antibody and analyzed by microarray hybridization
2016-03-29 | E-GEOD-79649 | biostudies-arrayexpress
Project description:We performed an integrated analysis of RNA and proteins at the transition between naïve ES cells and cells primed to differentiate. During this transition, mRNAs coding for chromatin regulators were specifically released from translational inhibition mediated by RNA-Induced Silencing Complex (RISC). This suggests that, prior to differentiation, the propensity of ES cells to change their epigenetic status is hampered by RNA interference. The expression of these chromatin regulators was reinstated following acute inactivation of RISC, and it correlated with loss of stemness markers and activation of early cell differentiation markers in treated ES cells. We evaluated ribosome occupancy of mRNAs in embryonic stem cells and Epiblast-Like Aggregates by means of polysome profiling with a modified Translating Ribosome Affinity Purification protocol (TRAP).
2016-03-29 | E-GEOD-79653 | biostudies-arrayexpress
Project description:Identification of differentiation status of human embryonic stem cell cultures.
| PRJNA114969 | ENA
Project description:We performed an integrated analysis of RNA and proteins at the transition between naïve ES cells and cells primed to differentiate. During this transition, mRNAs coding for chromatin regulators were specifically released from translational inhibition mediated by RNA-Induced Silencing Complex (RISC). This suggests that, prior to differentiation, the propensity of ES cells to change their epigenetic status is hampered by RNA interference. The expression of these chromatin regulators was reinstated following acute inactivation of RISC, and it correlated with loss of stemness markers and activation of early cell differentiation markers in treated ES cells. We evaluated global miRNA profiles of embryonic stem cells cultured in either 10%FCS+LIF or 2i+LIF and of Epiblast-Like Aggregates derived from ES cells in 10%FCS+LIF or 2iL+LIF.
2016-03-29 | E-GEOD-79654 | biostudies-arrayexpress
Project description:Pluripotent stem cells provide a powerful system to dissect the underlying molecular dynamics that regulate cell fate changes during mammalian development. Here we report the integrative analysis of genome wide binding data for 38 transcription factors with extensive epigenome and transcriptional data across the differentiation of human embryonic stem cells to the three germ layers. We describe core regulatory dynamics and show the lineage specific behavior of selected factors. In addition to the orchestrated remodeling of the chromatin landscape, we find that the binding of several transcription factors is strongly associated with specific loss of DNA methylation in one germ layer and in many cases a reciprocal gain in the other layers. Taken together, our work shows context-dependent rewiring of transcription factor binding, downstream signaling effectors, and the epigenome during human embryonic stem cell differentiation. 200 ChIP-seq experiments profiling 38 transcription factors (TFs) and several chromatin marks in 5 cell types--male human ES cell line HUES64 and directed differentiation of HUES64 towards mesendoderm (dMS, 12 hours), endoderm (dEN, 120 hours), mesoderm (dME, 120 hours), and ectoderm (dEC, 120 hours). In addition, three ES cell lines were derived with shRNA mediated knockdown of GATA4 and differention toward endoderm (dEN_shGATA4) and mesoderm (dME_shGATA4). These cell lines were used for MNChIP-seq of GATA4, SMAD1, and H3K27Ac and for 4 RRBS experiments in GATA4 knockdown and control cell lines.
2015-02-19 | E-GEOD-61475 | biostudies-arrayexpress