Transcription profiling of human Ishikawa cells treated with 17-alpha-estradiol
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Jay Patrick Tiesman
PROVIDER: E-GEOD-11869 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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2009-08-23 | E-GEOD-17624 | biostudies-arrayexpress
Project description:This study provides a comprehensive evaluation of changes in gene expression during treatment with Genistein in vitro. Ishikawa cells were maintained and grown (to confluency or at a desired cell density between 500,000 - 1 million cells/mL) in DMEM/F-12 Medium (supplemented with 10% Fetal Bovine Serum + 1X penicillin/streptomycin) in xenoestrogen-free Corning plasticware. Cells were gently washed in warm PBS and transferred to phenol red-free DMEM/F-12 Medium (supplemented with 10% Charcoal-Stripped Fetal Bovine Serum + 1X penicillin/streptomycin) in Corning Cell Culture Cluster wells overnight and then challenged with 10pM (very low, vL), 1 nM (low, L), 10nM (high, H), and 1uM (very high, vH) levels of Genistein. Prior to collection, cells were washed in warm PBS, resuspended & briefly incubated in TRI-Reagent, & finally collected (in quintuplicate replicates) at time each specific time point: 8 hours, 24 hours, and 48 hours. Following RNA isolation, the best RNA yields for each quadruplicate set was selected for target preparation and GeneChip processing. 60 total samples: 5 Doses [Vehicle Control, Very Low (1 pM), Low (100 pM), High (1 nM), Very High (1 uM)]; 3 Timepoints [8 hour, 24 hour, 48 hour]; 4 Replicates each
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Project description:Transcriptome analysis of MCF-7 cells exposed for 48 hours to various concentrations of xenoestrogen chemicals. Although biological effects of endocrine disrupting chemicals (EDCs) are often observed at unexpectedly low doses with occasional non-monotonic dose-response characteristics, transcriptome-wide profiles of sensitivities or dose-dependent behaviors of the EDC responsive genes have remained unexplored. Here, we describe expressome analysis for the comprehensive examination of dose-dependent gene responses and its applications to characterize estrogen responsive genes in MCF-7 cells. Transcriptomes of MCF-7 cells exposed to varying concentrations of representative natural and xenobiotic estrogens for 48 hours were determined by microarray and used for computational calculation of interpolated approximations of estimated transcriptomes for 300 doses uniformly distributed in log space for each chemical. The entire collection of these estimated transcriptomes, designated as the expressome, has provided unique opportunities to profile chemical-specific distributions of ligand sensitivities for large numbers of estrogen responsive genes, revealing that at low concentrations estrogens generally tended to suppress rather than to activate transcription. Gene ontology analysis demonstrated distinct functional enrichment between high- and low-sensitivity estrogen responsive genes, supporting the notion that a single EDC chemical can cause qualitatively distinct biological responses at different doses. Expressomal heatmap visualization of dose-dependent induction of Bisphenol A-inducible genes showed a weak gene activation peak at a very low concentration range (ca. 0.1 nM) in addition to the main, strong gene activation peak at and above 100 nM. Thus, expressome analysis is a powerful approach to understanding the EDC dose-dependent dynamic changes in gene expression at the transcriptomal level, providing important information on the overall profiles of ligand sensitivities and non-monotonic responses. Subconfluent density of MCF-7 cells were exposed to various concentrations of xenoestrogen chemicals for 48 hours and then subjected to transcriptomal analysis using Affymetrix U133 version 2 plus microarray.
2013-09-10 | E-GEOD-50705 | biostudies-arrayexpress
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