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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Yy1 activity in mouse embryonic stem cells

ABSTRACT: This SuperSeries is composed of the following subset Series: GSE31784: Expression changes in Yy1 knock down mouse embryonic stem cells GSE31785: Yy1 occupancy of mouse ES cell genome Refer to individual Series

ORGANISM(S): Mus musculus

SUBMITTER: Diego Pasini

PROVIDER: E-GEOD-31786 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Yin Yang 1 extends the Myc-related transcription factors network in embryonic stem cells.

Vella Pietro P Barozzi Iros I Cuomo Alessandro A Bonaldi Tiziana T Pasini Diego D

Nucleic acids research 20111230 8

The Yin Yang 1 (YY1) transcription factor is a master regulator of development, essential for early embryogenesis and adult tissues formation. YY1 is the mammalian orthologue of Pleiohomeotic, one of the transcription factors that binds Polycomb DNA response elements in Drosophila melanogaster and mediates Polycomb group proteins (PcG) recruitment to DNA. Despite several publications pointing at YY1 having a similar role in mammalians, others showed features of YY1 that are not compatible with P ...[more]

PMID: 22210892

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Expression changes in Yy1 knock down mouse embryonic stem cells

Project description:We have determined the global gene expression upon loss of function of the Yy1 transcription factor in mouse embryonic stem cells Total RNA was extracted from ES cells transiently transfected with yy1-specific or scrampled-control siRNA oligos 48 hr post-transfection.

2012-01-04 | E-GEOD-31784 | biostudies-arrayexpress

Ogt chromatin recruitment is mediated by TET proteins in mouse ES cells [expression array]

Project description:O-linked N-acetylglucosamine (O-GlcNAc ) transferase (OGT) activity is essential for embryonic stem (ES) cell viability and mouse development. OGT is present in both cytoplasm and nucleus of different cell types and mediates serine or threonine glycosylation. The Ogt gene locus resides on the X-chromosome and its activity is required for the viability of male ES cells. Using Ogt conditional knock out (KO) ES cells it was shown the failure of establishing stable KO ES clones further suggesting that Ogt activity is required for ES cell self-renewal and pluripotency. For understanding these changes, we performed global gene expression upon silencing of Ogt mediated by esiRNA in mouse Embryonic Stem Cells. Total RNA was extracted from E14 ES cells (derived from Ola129 mice) transiently transfected with Ogt specific and control esiRNA oligos 48 hrs. post-transfection.

2013-01-06 | E-GEOD-39321 | biostudies-arrayexpress

Ogt chromatin recruitment is mediated by TET proteins in mouse ES cells

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-01-06 | E-GEOD-39323 | biostudies-arrayexpress

The Histone Methyltransferase Wbp7 Controls Macrophage Function through GPI Glycolipid Anchor Synthesis. [Expression Profile]

Project description:Histone methyltransferases catalyze site-specific deposition of methyl groups, enabling recruitment of transcriptional regulators. In mammals, trimethylation of lysine 4 in histone H3, a modification localized at the transcription start sites of active genes, is catalyzed by six enzymes (SET1a and SET1b, MLL1M-bM-^@M-^SMLL4) whose specific functions are largely unknown. By using a genomic approach, we found that in macrophages, MLL4 (also known as Wbp7) was required for the expression of Pigp, an essential component of the GPI-GlcNAc transferase, the enzyme catalyzing the first step of glycosylphosphatidylinositol (GPI) anchor synthesis. Impaired Pigp expression in Wbp7-/- macrophages abolished GPI anchor-dependent loading of proteins on the cell membrane. Consistently, loss of GPI-anchored CD14, the coreceptor for lipopolysaccharide (LPS) and other bacterial molecules, markedly attenuated LPS-triggered intracellular signals and gene expression changes. These data link a histone-modifying enzyme to a biosynthetic pathway and indicate a specialized biological role for Wbp7 in macrophage function and antimicrobial response. Gene expression profiles for bone marrow-derived macrophages (BMDM) from either Wbp7+/- (HET) or Wbp7-/- (KO). Cells were left untreated or challenged with lipopolysaccharide (LPS) for 2hrs or 4hrs. Each genotype-treatment combination were performed in triplicate.

2012-04-08 | E-GEOD-30971 | biostudies-arrayexpress

HDAC3 requirement for the inflammatory gene expression program in macrophages [gene expression]

Project description:Pan-Hdac inhibitors (HDACi) are endowed with a potent anti-inflammatory activity, but the relative role of each of the eleven Hdac proteins sensitive to HDACi to the inflammatory gene expression program is unknown. Using an integrated genomic approach we found that Hdac3-deficient macrophages are unable to activate almost half of the inflammatory gene expression program when stimulated with lipopolysaccharide (LPS). A large part of the activation defect is due to loss of basal and LPS-inducible expression of IFNb, which in basal cells maintains Stat1 protein levels, and after stimulation acts in an autocrine/paracrine manner to promote a secondary wave of Stat1-dependent gene expression. We show that loss of Hdac3-mediated repression of nuclear receptors leads to hyperacetylation of thousands of genomic sites and associated gene derepression. The upregulation of the constitutively expressed prostaglandin endoperoxide synthase, Ptgs1 (Cox-1), has a causative role in the phenotype, since its chemical inhibition reverts the Ifnb activation defect. These data may have relevance for the use of selective Hdac inhibitors as anti-inflammatory agents. Gene expression profiles for bone marrow-derived macrophages from either HDAC3 +/- (wt) or HDAC3 -/- (KO). Cells were left untreated or challenged with lipopolysaccharide (LPS) for 4hrs. Each genotype-treatment combination was performed in triplicate.

2012-07-08 | E-GEOD-33162 | biostudies-arrayexpress

Polycomb proteins link Proliferation with DNA Replication

Project description:Polycomb proteins control proliferation and cellular transformation regulating DNA replication independently of cell cycle checkpoints Total RNA was extracted from MEF cells (derived from Ola129 mice) transiently transfected with Ezh2 specific and control esiRNA oligos 48 hrs. post-transfection.

2014-04-15 | E-GEOD-48520 | biostudies-arrayexpress

The Histone Methyltransferase Wbp7 Controls Macrophage Function through GPI Glycolipid Anchor Synthesis

Project description:This SuperSeries is composed of the following subset Series: GSE30971: The Histone Methyltransferase Wbp7 Controls Macrophage Function through GPI Glycolipid Anchor Synthesis. [Expression Profile] GSE30972: The Histone Methyltransferase Wbp7 Controls Macrophage Function through GPI Glycolipid Anchor Synthesis. [ChIP_seq] Refer to individual Series

2012-04-08 | E-GEOD-30973 | biostudies-arrayexpress

Gene expression profiles in Elastin (Eln+/-) mouse aorta and aortic valve tissue

Project description:Elastin wild type Eln+/+ and Eln+/- mouse aorta and aortic valve tissue. In the study, we demonstrated differential gene expression in juvenile elastin deficient mouse valve tissue. In the study, we hybridized RNA from Elastin wild type (Eln+/+) aorta tissue, elastin wild type (Eln+/+) aortic valve tissue, elastin (Eln+/-) aorta tissue and elastin (Eln+/-) aortic valve tissue to Affymetrix GeneChip Mouse Genome 430 2.0 Array

2009-11-30 | E-GEOD-16012 | biostudies-arrayexpress

HDAC3 requirement for the inflammatory gene expression program in macrophages

Project description:This SuperSeries is composed of the following subset Series: GSE33162: HDAC3 requirement for the inflammatory gene expression program in macrophages [gene expression] GSE33163: HDAC3 requirement for the inflammatory gene expression program in macrophages [ChIP_Seq] Refer to individual Series

2012-07-08 | E-GEOD-33164 | biostudies-arrayexpress

Expression data from Ring1A(-/-);Ring1B(fl/fl);R26::CreERT2 ES cells expressing either of mock, WT or mutant Ring1B construct before or after OHT treatment

Project description:We used microarrays to investigate the restoration of repression of PRC1 target gene expression in Ring1A/B-dKO ES cells stably expressing either of mock, WT or mutant Ring1B construct. Total RNAs were extracted from the respective ES cells, and were subjected to microarray analysis using Affymetrix GeneChip Mouse Genome 430A 2.0 arrays

2012-06-10 | E-GEOD-38224 | biostudies-arrayexpress

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