Ontology highlight
ABSTRACT:
PROVIDER: PRJNA507603 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8261790.fastq.gz | Fastqsanger.gz | |||
| SRR8261790_1.fastq.gz | Fastqsanger.gz | |||
| SRR8261790_2.fastq.gz | Fastqsanger.gz | |||
| SRR8261800_1.fastq.gz | Fastqsanger.gz | |||
| SRR8261800_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 59 |
Similar Datasets
Project description:mouse embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells were compared via metabolomic analysis
2018-08-02 | MSV000082680 | GNPS
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:The aim of this project is to differentiate human embryonic stem cells to an extra-embryonic fate, specifically the hypoblast. This is of uttermost importance given the current lack of human hypoblast stem cells.
We hypothesized that the pluripotent characteristics of the starting human embryonic stem cell population may dictate the competency for extra-embryonic cell fate specification. Based on this hypothesis and using human embryonic stem cells maintained in different naïve-like culture regimes, we have now developed conditions that allow the differentiation of human embryonic stem cells to a stable GATA6+ SOX2- population. This suggests that these cells may be putative human hypoblast stem cells. To validate this finding here we propose to perform RNA sequencing experiments of the differentiated human embryonic stem cells. By comparing their RNA expression profile to the single cell sequencing data of the human embryo that we are currently generating, we will be able to determine the identity of our GATA6+ SOX2- cells, and establish whether they represent the in vivo human hypoblast.
| EGAS00001003571 | EGA
Project description:Chavez2009 - a core regulatory network of OCT4 in human embryonic stem cells
A core OCT4-regulated network has been identified as a test case, to analyase stem cell characteristics and cellular differentiation.
This model is described in the article:
In silico identification of a core regulatory network of OCT4 in human embryonic stem cells using an integrated approach.
Chavez L, Bais AS, Vingron M, Lehrach H, Adjaye J, Herwig R
BMC Genomics, 2009, 10:314
Abstract:
BACKGROUND: The transcription factor OCT4 is highly expressed in pluripotent embryonic stem cells which are derived from the inner cell mass of mammalian blastocysts. Pluripotency and self renewal are controlled by a transcription regulatory network governed by the transcription factors OCT4, SOX2 and NANOG. Recent studies on reprogramming somatic cells to induced pluripotent stem cells highlight OCT4 as a key regulator of pluripotency.
RESULTS: We have carried out an integrated analysis of high-throughput data (ChIP-on-chip and RNAi experiments along with promoter sequence analysis of putative target genes) and identified a core OCT4 regulatory network in human embryonic stem cells consisting of 33 target genes. Enrichment analysis with these target genes revealed that this integrative analysis increases the functional information content by factors of 1.3 - 4.7 compared to the individual studies. In order to identify potential regulatory co-factors of OCT4, we performed a de novo motif analysis. In addition to known validated OCT4 motifs we obtained binding sites similar to motifs recognized by further regulators of pluripotency and development; e.g. the heterodimer of the transcription factors C-MYC and MAX, a prerequisite for C-MYC transcriptional activity that leads to cell growth and proliferation.
CONCLUSION: Our analysis shows how heterogeneous functional information can be integrated in order to reconstruct gene regulatory networks. As a test case we identified a core OCT4-regulated network that is important for the analysis of stem cell characteristics and cellular differentiation. Functional information is largely enriched using different experimental results. The de novo motif discovery identified well-known regulators closely connected to the OCT4 network as well as potential new regulators of pluripotency and differentiation. These results provide the basis for further targeted functional studies.
This model is hosted on BioModels Database
and identified
by: MODEL1305010000
.
To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource
for published quantitative kinetic models
.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to the public
domain worldwide. Please refer to CC0 Public Domain
Dedication
for more information.
2005-01-01 | MODEL1305010000 | BioModels
Project description:The aim of this project is to differentiate human embryonic stem cells to an extra-embryonic fate, specifically the hypoblast. This is of uttermost importance given the current lack of human hypoblast stem cells.
We hypothesized that the pluripotent characteristics of the starting human embryonic stem cell population may dictate the competency for extra-embryonic cell fate specification. Based on this hypothesis and using human embryonic stem cells maintained in different naïve-like culture regimes, we have now developed conditions that allow the differentiation of human embryonic stem cells to a stable GATA6+ SOX2- population. This suggests that these cells may be putative human hypoblast stem cells. To validate this finding here we propose to perform RNA sequencing experiments of the differentiated human embryonic stem cells. By comparing their RNA expression profile to the single cell sequencing data of the human embryo that we are currently generating, we will be able to determine the identity of our GATA6+ SOX2- cells, and establish whether they represent the in vivo human hypoblast.
This dataset contains all the data available for this study on 2020-04-20.
| EGAD00001006056 | EGA
Project description:Global gene expression data of human embryonic stem cell-, human induced pluripotent stem cell- and bone marrow-derived mesenchymal progenitor cells before and after culture onto osteoinductive scaffolds in perfusion bioreactors. The hypothesis tested in the present study was that perfusion culture in bioreactors influenced the expression levels of several genes involved in proliferation and osteogenic differentiation. Results provide important information of the response of human embryonic stem cell-, human induced pluripotent stem cell- and bone marrow-derived mesenchymal progenitor cell to osteogenic stimulation under perfusion cultures, such as genes involved in cell proliferation and division as well as osteogenic differentiation and bone development. Total RNA obtained from human embryonic stem cell-, human induced pluripotent stem cell- and bone marrow-derived mesenchymal progenitor cells before and after culture under osteogenic conditions in perfusion bioreactors for 5 weeks.
2013-04-24 | E-GEOD-46315 | biostudies-arrayexpress
Project description:Gene expression profiles were generated with Illumina arrays for untreated human mesenchymal stem cells and also Argonaute1 bound mRNAs in the same cells. In addition gene expression profiles were generated for the human embryo cell line H1 before and after differentiation along the neural lineage. NOTE: assays for human embryonic stem cells before and after differentiation were added in July 2014 and data files for the mesenchymal stem cells were updated.
2010-12-20 | E-TABM-1001 | biostudies-arrayexpress
Project description:RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of human mesenchymal stem cells differentiation from human embryonic stem cells and adult bone marrow mesenchymal stem cells
| PRJNA413815 | ENA
Project description:TimEX from human embryonic stem cells, mesenchymal stem cells, and erythroid cells
| PRJNA121555 | ENA