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Expression data from undifferentiated human ES cell line, khES3, grown using complete or methionine deprived media and ES cell derived endoderm

ABSTRACT: In undifferentiated human ES cells, 5hr Met deprivation (delta Met) led to decreased proliferation, and prolonged 24hr Met deprivation resulted in G0-G1 phase cell cycle arrest, which then led to apoptosis. We used microarrays to detail the molecular mechanism of cell-death caused by Met deprivation in undifferentiated ES cells and checked the difference of Met cycle relate gene expression between undifferentiated human ES cells and ES cell derived endoderm.

ORGANISM(S): Homo sapiens

PROVIDER: GSE55283 | GEO | 2014/04/17

SECONDARY ACCESSION(S): PRJNA239200

REPOSITORIES: GEO

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Expression data from undifferentiated human ES cell line, khES3, grown using complete or methionine deprived media and ES cell derived endoderm

Project description:In undifferentiated human ES cells, 5hr Met deprivation (delta Met) led to decreased proliferation, and prolonged 24hr Met deprivation resulted in G0-G1 phase cell cycle arrest, which then led to apoptosis. We used microarrays to detail the molecular mechanism of cell-death caused by Met deprivation in undifferentiated ES cells and checked the difference of Met cycle relate gene expression between undifferentiated human ES cells and ES cell derived endoderm. Cells were harvested at undifferentiated or differentiated stages for RNA extraction and hybridization on Affymetrix microarrays. We performed gene expression profiles of undifferentiated khES3 cells cultured in complete (compl) or Met-deprived conditions (deltaMet) for 5 or 24 hr. And 0hr untreated cells and endoderm cells were used as a comparison

2014-04-17 | E-GEOD-55283 | biostudies-arrayexpress

Expression data from undifferentiated human iPS cell line, 201B7

Project description:In undifferentiated human ES cells, 5hr Met deprivation (delta Met) led to decreased proliferation, and promote differentiation We used microarrays to detail the mollecular mechanism of cell-death caused by Met deprivation in undifferentiated iPS cells.

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Expression data from undifferentiated human ES cell line, khES3 grown using complete, leucine or lysine deprived media

2014-04-17 | GSE55284 | GEO

Expression data from undifferentiated human ES cell line, khES3 grown using complete, leucine or lysine deprived media

Project description:In undifferentiated human ES cells, 48hr Leucine deprivation (delta Leu) or Lysine deprivation (delta Lys) led to apoptosis. We used microarrays to detail the mollecular mechanism of cell-death caused by Leu, Lys deprivation in undifferentiated ES cells. Cells were harvested at undifferentiated stages for RNA extraction and hybridization on Affymetrix microarrays. We performed gene expression profiles of undifferentiated khES3 cells cultured in complete (comple),Leu or Lys deprivation for 5 hr.

2014-04-17 | E-GEOD-55284 | biostudies-arrayexpress

Loss of PRC2 subunits primes lineage choice during exit of pluripotency

Project description:Mouse embryoid body differentiation with single-cell analyses of timepoints 0, 4, 7 and 10. Bulk-RNA seq of directed differentiation of mouse embryonic stem cells from day 0, 5hr, 24hr and 48hrs.

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RNA-seq of human induced pluripotent cells treated with short-term Met deprival

Project description:Human iPSCs require high amounts of methionine (Met). Met deprivation results in a rapid decrease in intracellular S-adenosyl-methionine (SAM), poising human iPSCs for differentiation and leading to apoptosis of undifferentiated cells. Met deprivation triggers a rapid metabolite change, including SAM, followed by reversible epigenetic modification. We show here that short-term Met deprivation impairs pluripotency network through epigenetic modification. The trimethylation of lysine 4 on histone H3 (H3K4me3) was dramatically affected compared to other histone modifications. Transcription start site (TSS) region of key pluripotent genes such as NANOG and OCT3/4 are specifically impacted upon short-term Met deprivation. Gene expression levels of these genes decreased, correlating to the loss of H3K4me3 marks. Upon differentiation, Met deprivation triggers a loss of the H3K27me3 in many mesendodermal genes, thereby switching from a bivalent to monovalent (H3K4me3) state. We concluded that Met metabolism maintains the pluripotent network with histone marks, and their loss potentiates differentiation.

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ChIP-seq of human induced pluripotent cells treated with short-term Met deprival

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SSEA4 sorted I-6 Human ES cells

Project description:Human ES cell line I-6 was cultured in standard conditions to maintain an undifferentiated, self renewing phenotype. The cells were sorted based upon their expression of SSEA4, which is a marker of the undifferentiated, self renewing phenotype Keywords: other

2005-12-09 | GSE3794 | GEO

G9a deletion in female ES cells

Project description:G9a was deleted from female ES cells (16.7 Tsix +/TST) . The effects were analyzed by RNA-seq and ChIP-Seq comparing undifferentiated and differentiated states.

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