Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Glucocorticoid receptor (GR) target genes in C2C12 myotubes

ABSTRACT: Analysis of C2C12 myotubes treated with dexamethasone (Dex) for 6 or 24 hours. Dex is a synthetic glucorticoid receptor agonist. Results provide insight to the effect of glucocorticoids on myotubes. C2C12 myotubes were cultured in DMEM supplemented with 2% horse serum, and treated with 1 u? Dex or an equal volume (0.01% v/v of media) of vehicle control ethanol for 6 or 24 hours. Total cellular RNA was isolated utilizing the NucleoSpin RNA II kit (Macherey-Nagel). RNA isolates were first quantified by standard spectrophotometry, and then qualitatively evaluated by capillary electrophoresis employing the Bio-Rad Experion system per manufacturer’s instruction. The final labeled cRNA samples were hybridized overnight to Illumina mouseWG-6 BeadChip arrays, which was performed at UCSF Genomic Core. All treatments were done in triplicates and the same batch of microarrays were used for all treatments. The Illumina expression arrays were pre-processed using lumi package. The differential expression analysis was performed using the Limma package.

ORGANISM(S): Mus musculus

SUBMITTER: Jen-Chywan Wang

PROVIDER: E-GEOD-28840 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Similar Datasets

Project description:Estrogen receptorï? beta (ER beta) has potent anti-proliferative and anti-inflammatory properties, suggesting that ER beta-selective agonists might be a new class of therapeutic and chemopreventative agents. To understand how ER beta regulates genes, we identified genes regulated by the unliganded and liganded forms of ER alpha and ER beta in U2OS cells. Microarray data demonstrated that virtually no gene regulation occurred with unliganded ER alpha, whereas many genes were regulated by estradiol (E2). These results demonstrate ER alpha requires a ligand to regulate a single class of genes. In contrast, ER beta regulated three classes of genes. Class I genes were regulated primarily by unliganded ER beta. Class II genes were regulated only with E2, whereas Class III genes were regulated by both unliganded ER beta and E2. There were 453 Class I genes, 258 Class II genes and 83 Class III genes. To explore the mechanism whereby ER beta regulates different classes of genes ChIP-seq was performed to identify ER beta binding sites and adjacent transcription factor motifs in regulated genes. AP1 binding sites were more enriched in Class I genes, whereas ERE, NFKB1 and SP1 sites were more enriched in class II genes. ER beta bound to all three classes of genes demonstrating that ER beta binding is not responsible for differential regulation of genes by unliganded and liganded ER beta. The coactivator, NCOA2 was differentially recruited to several target genes. Our findings indicate that the unliganded and liganded forms of ER beta regulate three classes of genes by interacting with different transcription factors and coactivators. U2OS cell lines are stably transfected with a doxycycline-inducible ER alpha or beta. 18 samples are analyzed with triplicate for each of the 6 conditions. The 6 conditions include ER alpha transfected without doxycycline added, ER alpha transfected with doxycycline added, ER alpha transfected with doxycycline added and E2 treatment, ER beta transfected without doxycycline added, ER beta transfected with doxycycline added, and ER beta transfected with doxycycline added and E2 treatment.

Dataset Information

Glucocorticoid receptor (GR) target genes in C2C12 myotubes

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure