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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of human embryonic stem cells treated with BMP4 in chemically-defined medium, with and without inhibitors of Activin and FGF signalling to investigate the induction of extra-embryonic tissue differentiation by BMP signalling

ABSTRACT: Gene expression microarray analysis of hESCs treated with BMP4 in chemically-defined medium, with and without inhibitors of Activin and FGF signalling (which maintain pluripotency), to investigate the induction of extra-embryonic tissue (trophectoderm) differentiation by BMP signalling.

ORGANISM(S): Homo sapiens

SUBMITTER: Matthew Trotter

PROVIDER: E-MEXP-1192 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Early cell fate decisions of human embryonic stem cells and mouse epiblast stem cells are controlled by the same signalling pathways.

Vallier Ludovic L Touboul Thomas T Chng Zhenzhi Z Brimpari Minodora M Hannan Nicholas N Millan Enrique E Smithers Lucy E LE Trotter Matthew M Rugg-Gunn Peter P Weber Anne A Pedersen Roger A RA

PloS one 20090630 6

Human embryonic stem cells have unique value for regenerative medicine, as they are capable of differentiating into a broad variety of cell types. Therefore, defining the signalling pathways that control early cell fate decisions of pluripotent stem cells represents a major task. Moreover, modelling the early steps of embryonic development in vitro may provide the best approach to produce cell types with native properties. Here, we analysed the function of key developmental growth factors such a ...[more]

PMID: 19564924

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Transcription profiling of human embryonic stem cells and their differentiated progeny grown in chemically defined conditions

Project description:Comparison of H9 human embryonic stem cells, grown in chemically defined and animal-product free conditions, with their differentiated progeny - mesendodermal progenitors arisen as the result of changes made to chemically defined hESC growth conditions. Contributes to a larger work on the use of chemically defined growth conditions to direct hESC differentiation.

2009-07-31 | E-MEXP-930 | biostudies-arrayexpress

Transcription profiling of human embryonic stems cells grown in chemically defined medium supplemented with Activen and FGF or FGF2 and SB431542 to identify genes controlled by Activin/Nodal signalling

Project description:Human Embryonic Stem Cells (hESC) grown in chemically defined medium (CDM) supplemented with Activin and FGF were compared to hESCs grown for 48 hours in CDM supplemented with FGF2 and SB431542, an inhibitor of Activin/Nodal signalling. The objective of this experiment was to discover the identity of genes controlled by Activin/Nodal signalling in hESCs.<br><br>

2009-03-14 | E-MEXP-1741 | biostudies-arrayexpress

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Project description:Transcriptional profiling of H9 human embryonic stem cells differentiated towards early endoderm over 72 hours in chemically defined media.

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Project description:Human embryonic stem cells differentiated into endoderm progenitors in chemically-defined media.

2010-04-02 | E-MEXP-2373 | biostudies-arrayexpress

Pluripotency Factors Regulate Definitive Endoderm Specification through Eomesodermin

Project description:Understanding the molecular mechanisms controlling early cell fate decisions in mammals is a major objective towards the development of robust methods for the differentiation of human pluripotent stem cells into clinically relevant cell types. Here, we used human embryonic stem cells (hESCs) to study specification of definitive endoderm in vitro. Using a combination of whole genome expression and ChIP-seq analyses, we established a hierarchy of transcription factors regulating endoderm specification. Importantly, pluripotency factors, namely NANOG, OCT4 and SOX2 have an essential function in this network by actively directing differentiation. Indeed, these transcription factors control the expression of EOMES, which marks the onset of endoderm specification. In turn, EOMES interacts with SMAD2/3 to initiate the transcriptional network governing endoderm formation. Together, these results provide for the first time a comprehensive molecular model connecting the transition from pluripotency to endoderm specification during mammalian development. ChIP-Seq of Eomesodermin binding in human embyonic stem cells, differentiated towards an endodermal fate for 48h in chemically-defined culture media. Includes an input DNA control. Supplementary file GSE26097_README.txt contains descriptions of the raw data files and processed data files.

2011-01-25 | E-GEOD-26097 | biostudies-arrayexpress

Vallier D4.5 SB

Project description:Gene expression profiling experiment to identify genes up and down regulated by the presence of Activin during pancreatic specification.

2011-11-12 | E-MTAB-606 | biostudies-arrayexpress

Cheung SMC 2011

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BRACHYURY knockdown in differentiating hESCs

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Activin/Nodal signalling controls divergent transcriptional networks in pluripotent and endoderm progenitors.

Project description:Activin/Nodal signalling is necessary to maintain pluripotency of human Embryonic Stem Cells (hESCs) and to induce their differentiation towards endoderm. However, the mechanisms by which Activin/Nodal signalling achieves these opposite functions remain unclear. To unravel these mechanisms, we examined the transcriptional network controlled in hESCs by Smad2 and Smad3 which represent the direct effectors of Activin/Nodal signalling. These analyses reveal that Smad2/3 participate in the control of the core transcriptional network characterising pluripotency which includes Oct-4, Nanog, FoxD3, Dppa4, Tert, Myc and UTF-1. In addition, similar experiments performed on endoderm cells confirm that a broad part of the transcriptional network directing differentiation is downstream of Smad2/3. Therefore, Activin/Nodal signalling appears to control divergent transcriptional networks in hESCs and in endoderm. Importantly, we observed an overlap between the transcriptional network downstream of Nanog and Smad2/3 in hESCs while functional studies showed that both factors cooperate to control the expression of pluripotency genes. Therefore, the effect of Activin/Nodal signalling on pluripotency and differentiation could be dictated by tissue specific Smad2/3 partners such as Nanog, explaining the mechanisms by which signalling pathways can orchestrate divergent cell fate decisions. Identification of Smad2/3 binding sites in pluripotent hESCs. 5 ChIP-Seq samples including 1 input control sample and 4 ChIP samples (two conditions x two replicates).

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