{"platform": 6, "owner": "ArrayExpress Uploader", "pop_total": 0, "species": "mouse", "factors": [{"GSM659775": {"KNOCKDOWN": "control", "OVEREXPRESSION": "none"}}, {"GSM659775": {"KNOCKDOWN": "control", "OVEREXPRESSION": "none"}}, {"GSM659775": {"KNOCKDOWN": "control", "OVEREXPRESSION": "none"}}, {"GSM659775": {"KNOCKDOWN": "control", "OVEREXPRESSION": "none"}}, {"GSM659779": {"KNOCKDOWN": "Tet1", "OVEREXPRESSION": "none"}}, {"GSM659779": {"KNOCKDOWN": "Tet1", "OVEREXPRESSION": "none"}}, {"GSM659779": {"KNOCKDOWN": "Tet1", "OVEREXPRESSION": "none"}}, {"GSM659779": {"KNOCKDOWN": "Tet1", "OVEREXPRESSION": "none"}}, {"GSM659783": {"KNOCKDOWN": "Tet1", "OVEREXPRESSION": "Nanog"}}, {"GSM659783": {"KNOCKDOWN": "Tet1", "OVEREXPRESSION": "Nanog"}}, {"GSM659783": {"KNOCKDOWN": "Tet1", "OVEREXPRESSION": "Nanog"}}, {"GSM659783": {"KNOCKDOWN": "Tet1", "OVEREXPRESSION": "Nanog"}}], "id": 6342, "ownerprofile_id": "arrayexpress_sid", "source": "http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26830", "summary_wrapped": "Epigenetic modification of the mammalian genome by DNA methylation (5-methylcytosine) has a profound impact on chromatin structure, gene...", "pubmed_id": 21451524, "owner_profile": "/profile/8773/arrayexpressuploader", "factor_count": 2, "sample_count": 12, "tags": ["cell", "chromatin", "genome"], "lastmodified": "Dec.12, 2014", "is_default": false, "geo_gds_id": "", "slug": "dual-functions-of-tet1-in-transcriptional-regulati", "geo_id_plat": "E-GEOD-26830_A-AFFY-45", "name": "Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells (mRNA)", "created": "Nov.11, 2014", "summary": "Epigenetic modification of the mammalian genome by DNA methylation (5-methylcytosine) has a profound impact on chromatin structure, gene expression and maintenance of cellular identity. Recent demonstration that members of the Ten-eleven translocation (Tet) family proteins can convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) raised the possibility that Tet proteins are capable of establishing a distinct epigenetic state. We have recently demonstrated that Tet1 is specifically expressed in murine embryonic stem (ES) cells and is required for ES cell self-renewal and maintenance. Using chromatin immunoprecipitation coupled with high-throughput DNA sequencing (ChIP-seq), here we show that Tet1 is preferentially bound to CpG-rich sequences at promoters of both transcriptionally active and Polycomb-repressed genes. Despite a general increase in levels of DNA methylation at Tet1 binding-sites, Tet1 depletion does not lead to down-regulation of all the Tet1 targets. Interestingly, while Tet1-mediated promoter hypomethylation is required for maintaining the expression of a group of transcriptionally active genes, it is also required for repression of Polycomb-targeted developmental regulators. Tet1 contributes to silencing of this group of genes by facilitating recruitment of PRC2 to CpG-rich gene promoters. Thus, our study not only establishes a role for Tet1 in modulating DNA methylation levels at CpG-rich promoters, but also reveals a dual function of Tet1 in promoting transcription of pluripotency factors as well as participating in the repression of Polycomb-targeted developmental regulators. Mouse ES cells infected with control knockdown (KD) or Tet1 KD  lentiviruses  were FACS-sorted for RNA extraction and hybridization on Affymetrix microarrays.  We also investigated the effect of Nanog overexpression (OE) in Tet1 KD mouse ES cells on dys-regulated Tet1 targets. We have collected four biologically independent replicates for each treatment.", "geo_gse_id": "E-GEOD-26830", "sample_source": "http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26830/samples/"}