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Genome-wide analysis of gene expression perturbed by Pontin shRNA in MCF7 subjected to normoxic and hypoxic conditions

ABSTRACT: In order to investigate the role of Pontin methylation on the expression of hypoxia responsive genes across the whole genome, we performed a microarray analysis from RNAs isolated from MCF7 cells expressing either control shRNA (shNS) or Pontin shRNA(shPontin) in normoxic and hypoxic conditions.

ORGANISM(S): Homo sapiens

PROVIDER: GSE27813 | GEO | 2011/12/02

SECONDARY ACCESSION(S): PRJNA137927

REPOSITORIES: GEO

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Genome-wide analysis of gene expression perturbed by Pontin shRNA in MCF7 subjected to normoxic and hypoxic conditions

Project description:In order to investigate the role of Pontin methylation on the expression of hypoxia responsive genes across the whole genome, we performed a microarray analysis from RNAs isolated from MCF7 cells expressing either control shRNA (shNS) or Pontin shRNA(shPontin) in normoxic and hypoxic conditions. MCF7 cells were transiently transfected with either non-specific shRNA or Pontin shRNA in replicates. Cells were grown for 24 hours before being exposed to either normoxic (21% Oxygen) or hypoxic condition (1% oxygen) for 6,9 hours. Cells were then lysed and RNA isolated.

2011-12-02 | E-GEOD-27813 | biostudies-arrayexpress

Genome-wide analysis of gene expression perturbed by reptin shRNA in MCF7 subjected to normoxic and hypoxic conditions

2010-07-13 | GSE15530 | GEO

Genome-wide analysis of gene expression perturbed by reptin shRNA in MCF7 subjected to normoxic and hypoxic conditions

Project description:In order to investigate the role of reptin methylation on the expression of hypoxia-responsive genes across the whole genome, we performed a microarray analysis from RNAs isolated from MCF7 cells expressing either control shRNA (shRNA) or reptin shRNA (shreptin) in normoxic and hypoxic conditions. MCF7 cells were transiently transfected with either non-specific shRNA or reptin shRNA in replicates. Cells were grown for 24 hours before being exposed to either normoxic (21% oxygen) or hypoxic (1% oxygen) conditions for 18 hours. Cells were then lysed and RNA was isolated.

2010-07-13 | E-GEOD-15530 | biostudies-arrayexpress

Genome-wide analysis of gene expression perturbed by reptin shRNA in MCF7 subjected to normoxic and hypoxic conditions

Project description: Not available

| S-ECPF-GEOD-15530 | biostudies-other

Lung Cancer Exosomes Hypoxic v Normoxic

Project description:Exosomes derived from NSCLC cells under normoxic or hypoxic conditions were compared to identify hypoxic associated enrichment of proteins in exosomes.

2023-03-10 | PXD038587 | Pride

Transcription profiling of human monocytes and monocyte-derived macrophages subjected to normoxic or hypoxic conditions

Project description:Microarray analysis was carried out on human monocytes (Mono) and monocyte-derived macrophages (MDM) (n = 4 donors) that were subjected to normoxic (N) or hypoxic (H) conditions. Purified human monocytes and their MDM were cultured for 24 h in CSF-1 (5000U/ml) under normoxic or hypoxic conditions.

2009-03-26 | E-MEXP-2104 | biostudies-arrayexpress

mRNA profiling of Pontin WT and RA under glucose starvation

Project description:To determine which genes are affected by methylated Pontin, we performed RNA-sequencing (RNA-seq) in Pontin WT and RA MEFs after glucose starvation.

2020-10-26 | GSE130069 | GEO

Expression data from MCF7 breast epithelial cells in normoxic and hypoxic conditions.

Project description:G9a is able to silence gene expression in hypoxic condition by increasing histone H3K9me2. We have identified a set of genes that are negatively regulated by G9a in hypoxia-dependent manner. In this dataset, we include the expression data obtained from MCF7 breast epithelial cells that have been transfected with control (WT) or G9a shRNAs (KD) and exposed to either normoxia or hypoxia. These data are used to obtain 829 genes that are differentially expressed in response to hypoxia, and 205 genes that are sentisive to G9a level. 4 samples were analysed. We generated comparisons between WT and KD in normoxic as well as hypoxic condition. Genes differentially expressed in hypoxic condition were selected followed by selection of genes that lose this differential expression upon G9a knockdown.

2015-12-31 | E-GEOD-59449 | biostudies-arrayexpress

Pontin Functions as A Transcriptional Co-activator for Retinoic Acid-induced HOX Gene Expression [GRO-seq]

Project description:Pontin is a AAA+ ATPase protein that has functions in various biological contexts including gene transcription regulation, chromatin remodeling, DNA damage sensing and repair, as well as assembly of protein and ribonucleoprotein complexes. Pontin is known to regulate the transcription of several important signaling pathways, including Wnt signaling. However, its role in early embryonic signaling regulation remains unclear. Retinoic acid (RA) signaling plays a central role in vertebrate development. Using an in vivo biotin tagging technology, we mapped the genome-wide binding pattern of Pontin before and after RA-induced differentiation in the pluripotent embryo carcinoma cell line NTEAR-2. Biotin ChIP-seq revealed significant changes in genome-wide Pontin binding sites upon RA stimulation. We also identified a substantial amount of overlapping binding peaks between Pontin and RARα, especially on all of the HOX gene loci (A-D clusters). Pontin knockdown experiments showed that its chromatin binding at the HOX gene clusters is required for RA-induced HOX gene expression. Furthermore, we performed Global Run-On sequencing (GRO-seq) to map de novo transcripts genome-wide and found that Pontin knockdown significantly diminished nascent HOX gene transcripts, indicating that Pontin regulates HOX gene expression at the transcriptional level. Finally, proteomic analysis demonstrated that Pontin associates with chromatin organization/remodeling complexes and various other functional complexes. Altogether, we have demonstrated that Pontin is a critical transcriptional co-activator for RA-induced HOX gene activation.

2021-06-16 | GSE162371 | GEO

Pontin Functions as A Transcriptional Co-activator for Retinoic Acid-induced HOX Gene Expression [ChIP-seq]

2021-06-16 | GSE162360 | GEO

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