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Unknown,Transcriptomics,Genomics,Proteomics

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H3K4me3 location in U937 cells

ABSTRACT: H3K4me3 enrichment at proximal promoter regions Keywords: ChIP-on-chip data We describe that RBP2 shows high correlation with the presence of H3K4me3. Biological replicates: chromatin immunoprecipitations were performed independently in parallel

ORGANISM(S): Homo sapiens

SUBMITTER: Elizaveta Benevolenskaya

PROVIDER: E-GEOD-10635 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-wide analysis of the H3K4 histone demethylase RBP2 reveals a transcriptional program controlling differentiation.

Lopez-Bigas Nuria N Kisiel Tomasz A TA DeWaal Dannielle C DC Holmes Katie B KB Volkert Tom L TL Gupta Sumeet S Love Jennifer J Murray Heather L HL Young Richard A RA Benevolenskaya Elizaveta V EV

Molecular cell 20080801 4

Retinoblastoma protein (pRB) mediates cell-cycle withdrawal and differentiation by interacting with a variety of proteins. RB-Binding Protein 2 (RBP2) has been shown to be a key effector. We sought to determine transcriptional regulation by RBP2 genome-wide by using location analysis and gene expression profiling experiments. We describe that RBP2 shows high correlation with the presence of H3K4me3 and its target genes are separated into two functionally distinct classes: differentiation-indepen ...[more]

PMID: 18722178

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RBP2 location analysis

Project description:RBP2 (JARID1A/RBBP2) enrichment at proximal promoter regions in differentiating promonocytic U937 cells and in the osteosarcoma SAOS-2 cells Keywords: differentiation treatment, ChIP-on-chip analysis We sought to determine transcriptional regulation by RBP2 genome-wide by using location analysis. We describe that RBP2 target genes are separated into two functionally distinct classes: differentiation independent and differentiation dependent genes.Three condition experiment, U937 cells treated with 100 nM 12-O-tetradeconoyl-phorbol 13-acetate (TPA) (Sigma) for two different time points (27 hrs and 96 hrs) and untreated (0 hrs time point or no TPA treatment). In addition, processed data for the unrelated SAOS-2 cells are included. Biological replicates: threechromatin immunoprecipitations (ChIP) performed independently in parallel

2010-06-20 | E-GEOD-10636 | biostudies-arrayexpress

RNA_Pol2_Ser5phospho_mES

Project description:Mouse embryonic stem cells were used to study RNA Polymerase 2 phosphorylation of Ser 5 IP. Duplicate whole genome mouse arrays of embryonic stem cells. RNA Polymerase II phosphoCTD (Serine 5) antibody was used in the experiment.

2011-10-03 | E-GEOD-17273 | biostudies-arrayexpress

Methylation profiling defines a widespread field defect in histologically normal prostate tissue associated with prostate cancer

Project description:We evaluated the presence of genome-wide epigenetic differences at 385,000 loci using Encode HG18 DNA methylation arrays in 5 non-tumor-associated (NTA) and 4 histologically undistinguished tumor-associated (TA) prostate tissues. We identified 615 probes to be differentially methylated (p<0.05) in TA prostate, with 537 (87%) hypomethylated and 78 (13%) hypermethylated. comparison of methylation in NTA to TA prostate tissue

2012-06-27 | E-GEOD-38982 | biostudies-arrayexpress

Cdk11-Cyclin L controls the assembly of the RNA polymerase II Mediator

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

2014-07-11 | E-GEOD-37962 | biostudies-arrayexpress

ChIP-chip from Ehrlichia chaffeensis-infected THP-1 cells with ankyrin repeat-containing protein, p200

Project description:Host genes interacting with ankyrin repeat-containing protein, p200, in Ehrlichia chaffeensis-infected monocytes. Chromatin immunoprecipitation (ChIP) together with microarray (chip) analysis demonstrated enrichment of relatively small subset (n=456) of host cell genes associated with molecular and biological processes, many of which are known to be altered during ehrlichial infection. Keywords: ChIP-chip Detection of genes with high signal enrichment by comparing the ratios of p200/input

2010-05-16 | E-GEOD-13464 | biostudies-arrayexpress

Binding pattern and chromatin modifications induced by AML1/ETO in human hematopoietic stem/progenitor cells

Project description:The AML1/ETO fusion protein, which is present in 10% to 15% of cases of acute myeloid leukemia, is known to repress myeloid differentiation genes through DNA binding and recruitment of chromatin-modifying proteins and transcription factors in target genes. ChIP-chip analysis of human hematopoietic stem/progenitor cells transduced with the AML1/ETO fusion gene enabled us to identify 1168 AML1/ETO target genes, 103 of which were co-occupied by HDAC1 and had lost the hyperacetylation at histone H4 marks and 264 of which showed a K9 trimethylation at histone H3. Enrichment of genes involved in hematopoietic differentiation and in specific signaling pathways was observed in the presence of these epigenetic modifications associated with an inactive chromatin status. Furthermore, AML1/ETO target genes had a significant correlation between the chromatin marks studied and transcriptional silencing. ChIP-chip comparison of human hematopoietic stem/progenitor cells (HSPCs) retrovirally transduced with the AML1/ETO fusion protein with HSPCs transduced with an empty vector (Mulloy et al., Blood, 2002) using antibodies tagging the AML1/ETO fusion protein, the HDAC1 protein, as well as H4Ac and H3K9m3 chromatin modifications.

2012-01-18 | E-GEOD-27663 | biostudies-arrayexpress

Rapid reprogramming of epigenetic and transcriptional profiles in mammalian culture systems

Project description:Comparison of the methylation profile of mouse embryonic fibroblasts (MEFs) before and during adaptation to cell culture conditions. Matched expression data is deposited under accession: E-MTAB-3172

2014-12-17 | E-MTAB-3176 | biostudies-arrayexpress

Rapid reprogramming of epigenetic and transcriptional profiles in mammalian culture systems

Project description:5-hmC profiling of mouse embryonic fibroblasts before and during adaptation to cell culture conditions using hMeDIP-chip

2014-12-17 | E-MTAB-3177 | biostudies-arrayexpress

Cdk11-Cyclin L controls the assembly of the RNA polymerase II Mediator [ChIP-chip]

Project description:The L-Mediator is a general co-activator of RNA Polymerase II transcription and is formed by the reversible association of the S-Mediator and the kinase module harbouring Cdk8. We describe the Cdk11-Lcp1 complex and show that its inactivation alter the global expression profiles in a very similar way than mutations of the kinase module. Cdk11 is broadly distributed onto chromatin and phosphorylate the Med27 and Med4 Mediator subunits on conserved residues. The inactivation of either Cdk11 or the mutation of its target residues on the Mediator leads to a strongly decreased association of the kinase module and the S-Mediator. The results show that Cdk11-Lcp1 regulates that assembly of the L-Mediator complex. Two independent immunoprecipitations were done for HA-tagged Cdk11 and each biological replicate was hybridized in duplicate on Agilent arrays using input DNA as the reference channel.

2014-07-11 | E-GEOD-37961 | biostudies-arrayexpress

Goat mammary gland differentiation during pregnancy

Project description:Development of mammary secretory epithelium and its functional differentiation occur during pregnancy under combined actions of ovarian steroids, pituitary hormones and growth factors. If the effect of these molecules is relatively well known, effect of differentiation factors expressed locally is not enough characterized. To understand local regulation of mammary tissue development and differentiation we realized transcriptional analysis on 5 physiological stages (4 during pregnancy and 1 during lactation). An appropriate experimental design was drawn to follow gene expression profiles during differentiation of mammary tissue. Results showed that at mid-pregnancy, mammary tissue was enough defferentiated into secretory epithelium to express milk protein genes and genes of the immune response system actors. But the secretoty activation of mammary epithelium was done only after parturition and wwas characterized by the expression of lipidogenesis genes. Keywords: time course, mammary gland differentiation, goat, pregnancy 18 samples, loop design

2010-05-16 | E-GEOD-14008 | biostudies-arrayexpress

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