Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

9 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression profile of Tet1 knockout mouse embryonic stem cells (mESCs)

ABSTRACT: Global gene expression profile of Tet1 knockout ES cells is compared to wild-type ES cells. All ES lines used are V6.5 (mix 129 C57BL6 backgound). 2 Tet1 KO mice compared to 1 Tet1 wild type mouse.

ORGANISM(S): Mus musculus

SUBMITTER: Albert Cheng

PROVIDER: E-GEOD-30748 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Tet1 is dispensable for maintaining pluripotency and its loss is compatible with embryonic and postnatal development.

Dawlaty Meelad M MM Ganz Kibibi K Powell Benjamin E BE Hu Yueh-Chiang YC Markoulaki Styliani S Cheng Albert W AW Gao Qing Q Kim Jongpil J Choi Sang-Woon SW Page David C DC Jaenisch Rudolf R

Cell stem cell 20110801 2

The Tet family of enzymes (Tet1/2/3) converts 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). Mouse embryonic stem cells (mESCs) highly express Tet1 and have an elevated level of 5hmC. Tet1 has been implicated in ESC maintenance and lineage specification in vitro but its precise function in development is not well defined. To establish the role of Tet1 in pluripotency and development, we have generated Tet1 mutant mESCs and mice. Tet1(-/-) ESCs have reduced levels of 5hmC and subtle ch ...[more]

PMID: 21816367

Similar Datasets

Gene expression profile of Tet1 knockout cortex and hippocampus

Project description:Global gene expression profile of Tet1 knocout cortex or hippocampus is compared to wild-type cortex or hippocampus. All mice used are naM-CM-/ve and of mixed 129 C57BL6 backgound. Tet1 KO in brain cortex and hippocampus

2013-09-01 | E-GEOD-48789 | biostudies-arrayexpress

Metastable pluripotent states in NOD mouse derived ES cells

Project description:Embryonic stem (ES) cells are isolated from the inner cell mass (ICM) of developing blastocysts, whereas epiblast stem cells (EpiSCs) are derived from the post-implantation epiblast and are characterized by a restricted developmental potential. Although certain mouse strains, such as the non-obese diabetic (NOD) mice, are considered “non-permissive” for ES cell derivation, they retain the capacity to generate EpiSCs. Using the NOD strain as a model, we characterized the stability of pluripotent states in cells generated by ICM explantation or direct in vitro reprogramming. We find that ES-like NOD stem cells can be captured in both approaches by providing exogenous constitutive expression of Klf4 or c-Myc transcription factors or small molecules that can replace these factors during in vitro reprogramming. The fully pluripotent NOD ES and iPS cells appear “metastable”, as the cells acquire an alternative EpiSC-like identity after removal of the exogenous factors, while reintroduction of these factors converts the cells back to ICM-like pluripotency. Our findings suggest that stem cells from different genetic backgrounds can assume distinct states of pluripotency in vitro, the stability of which is regulated by endogenous genetic determinants and can be modified by the continuous presence of defined exogenous factors. Gene expression profiling was performed in mouse ES, EpiSC and EpiSC-like cell lines.

2009-04-09 | E-GEOD-15603 | biostudies-arrayexpress

ESlncRNA (AK148461) over-expression on gene expression

Project description:We over-expressed ESlncRNA (AK148461) in fetal liver erythroid progenitor cells (Lin-cells), followed by microarray analysis to examine the global changes of gene expression level. We showed that ESlncRNA has an anti-apoptotic activity during mouse erythropoiesis. Compare the gene expression level in vector transduced fetal liver erythroid progenitor cells (Lin-cells) with that in ESlncRNA transduced fetal liver erythroid progenitor cells (Lin-cells).

2012-01-06 | E-GEOD-30279 | biostudies-arrayexpress

De novo DNA methylation by Dnmt3a and Dnmt3b is dispensable for nuclear reprogramming of somatic cells to a pluripotent state

Project description:Induced pluripotent stem cells (iPSCs) are generated from somatic cells by the transduction of defined transcription factors and involves dynamic changes in DNA methylation. While the reprogramming of somatic cells is accompanied by de-methylation of pluripotency genes, the functional importance of de novo DNA methylation has not been clarified. Here, using loss-of-function studies, we generated iPSCs from fibroblasts that were deficient in de novo DNA methylation mediated by Dnmt3a and Dnmt3b. These iPSCs reactivated pluripotency genes, underwent self-renewal and showed restricted developmental potential which was rescued upon re-introduction of Dnmt3a and Dnmt3b. We conclude that de novo DNA methylation by Dnmt3a and Dnmt3b is dispensable for nuclear reprogramming of somatic cells. RNA levels of Dnmt3ab deficient iPSC cell lines were compared to control iPSC cell lines

2011-05-16 | E-GEOD-28629 | biostudies-arrayexpress

Gene expression profile of Tet1 knockout mouse embryonic stem cells (mESCs)

Project description:Global gene expression profile of Tet1 knockout ES cells is compared to wild-type ES cells. All ES lines used are V6.5 (mix 129 C57BL6 backgound).

2011-08-01 | GSE30748 | GEO

Derivation of pre-X inactivation human embryonic stem cells under physiological oxygen concentrations

Project description:The presence of two active X chromosomes (XaXa) is a hallmark of the ground state of pluripotency specific to murine embryonic stem cells (ESCs). Human ESCs invariably exhibit signs of X chromosome inactivation (XCI) and are considered developmentally more advanced than their murine counterparts. We describe the establishment of the first XaXa hESCs derived under physiological oxygen concentrations. Using these cell lines we demonstrate that (1) differentiation of hESCs induces random XCI in a manner similar to murine ESCs, (2) exposure to atmospheric oxygen is sufficient to induce irreversible XCI and dramatic changes throughout the transcriptome, (3) the Xa exhibits heavy methylation of the XIST promoter region, and (4) XCI is associated with demethylation and transcriptional activation of XIST along with H3K27-me3 deposition across the Xi. These findings suggest that XaXa cells exist in the ICM of the human blastocyst and that this state is preserved in vitro through culture under physiological oxygen. Gene expression profiling was performed on human ES cell lines isolated and maintained under different oxygen concentrations

2010-11-10 | E-GEOD-20937 | biostudies-arrayexpress

The X-linked H3K27me3 demethylase Utx is required for embryonic development in a sex specific manner [Agilent array data]

Project description:Embryogenesis requires the timely and coordinated activation of developmental regulators. It has been suggested that the recently discovered class of histone demethylases (UTX and JMJD3) that specifically target the repressive H3K27me3 modification play an important role in the activation of M-bM-^@M-^\bivalentM-bM-^@M-^] genes in response to specific developmental cues. To determine the requirements for UTX in pluripotency and development, we have generated Utx null ES cells and mutant mice. The loss of UTX had a profound effect during embryogenesis. Utx null embryos had reduced somite counts, neural tube closure defects and heart malformation which presented between E9.5 and E13.5. Unexpectedly, homozygous mutant female embryos were more severely affected than hemizygous mutant male embryos. In fact, we observed the survival of a subset of UTX-deficient males which were smaller in size and had reduced life-span. Interestingly, these animals were fertile with normal spermatogenesis. Consistent with a mid-gestation lethality, UTX null male and female ES cells gave rise to all three germ layers in teratoma assays although sex-specific differences could be observed in the activation of developmental regulators in embryoid body assays. Lastly, ChIP-seq analysis revealed an increase in H3K27me3 in Utx null male ES cells. In summary, our data demonstrate sex-specific requirements for this X-linked gene while suggesting a role for UTY during development. Keywords: Expression profiling by array Four-condition experiment, Wt (V6.5) ES vs. RA-treated Wt (V6.5) ES cells; UtxKO ES vs RA-treated UtxKO ES cells. This Series represents the Agilent microarray data only (not ChIP-Seq).

2012-07-31 | E-GEOD-39473 | biostudies-arrayexpress

Mouse lung tumor tissue: Dnmt3a KO vs. Dnmt3a WT

Project description:Transcriptional profiling of mouse lung tumors comparing Dnmt3a KO/K-ras G12D mutant with Dnmt3a WT/K-ras G12D mutant. The goal is to search for the difference of mRNA abundance between Dnmt3a KO and WT tumors. Two-condition experiment, KO vs. WT tissure. Biological replicates: 12.

2011-10-25 | E-GEOD-32415 | biostudies-arrayexpress

Control of Embryonic Stem Cell State by Mediator and Cohesin (Agilent gene expression data)

Project description:The key transcription factors that control the embryonic stem cell gene expression program have been identified, but how they function to implement this program is not well understood. While screening for genes essential for maintenance of ES cell state, we identified many components of the Mediator and Cohesin complexes. Mediator and Cohesin were found to physically and functionally connect the enhancers and core promoters of active genes. An ES cell Mediator complex was found to copurify with Cohesin and its loading factor Nipbl, and normal levels of these proteins were essential for expression of the genes they occupy and for maintenance of ES cell state. See associated publication.

2010-08-12 | E-GEOD-22556 | biostudies-arrayexpress

Gene expression profile of Tet1 knockout cortex and hippocampus

Project description:Global gene expression profile of Tet1 knocout cortex or hippocampus is compared to wild-type cortex or hippocampus. All mice used are naïve and of mixed 129 C57BL6 backgound.

2013-09-01 | GSE48789 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data