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Series GSE7535 Query DataSets for GSE7535
Status Public on Mar 26, 2008
Title Toxicogenomic Analysis of Caenorhabditis elegans Reveals Genes Involved in the Resistance to Cadmium Toxicity
Organism Caenorhabditis elegans
Experiment type Expression profiling by array
Summary Exposure to cadmium is associated with a variety of human diseases. At low concentrations, cadmium activates the transcription of stress-responsive genes, which can prevent or repair the adverse effects caused by this metal. Using C. elegans, 290 genes were identified that are differentially expressed (≥1.5-fold) following a 4 or 24 hour exposure to cadmium. Several of these genes are known to be involved in metal detoxification, including mtl-1, mtl-2, cdr-1 and ttm-1, confirming the efficacy of the study. The majority, however, were not previously associated with metal-responsiveness and are novel. Gene Ontology analysis mapped these genes to cellular/ion trafficking, metabolic enzymes and proteolysis categories. RNAi-mediated inhibition of 50 cadmium-responsive genes resulted in an increased sensitivity to cadmium toxicity, demonstrating that these genes are involved in the resistance to cadmium toxicity. Several functional protein interacting networks were identified by interactome analysis. Within one network, the signaling protein KEL-8 was identified. Kel-8 protects C. elegans from cadmium toxicity in a mek-1 (MAPKK)-dependent manner. Because many C. elegans genes and signal transduction pathways are evolutionarily conserved, these results may contribute to the understanding of the functional roles of various genes in cadmium toxicity in higher organisms.
Keywords: gene expression time course
Overall design Total RNA was prepared from non-treated control nematodes and those exposed to 100 μM cadmium for 4 h and 24 h. For each condition, RNA samples were prepared from three independent cultures of C. elegans, and the RNA was isolated in triplicate. This generated nine replicates per treatment. RNA samples from cadmium-treated and control C. elegans were labeled using Low RNA Input Fluorescent Linear Amplification Kits following the manufacture’s protocols (Agilent Technologies). Labeled cRNAs were hybridization to Agilent C. elegans oligonucleotide microarrays. These microarrays contain target probes for the entire C. elegans genome, ~20,000 ORFs (Agilent Technologies). Dye-flips were performed for each pair of hybridizations resulting in a total of 36 hybridizations. Data was extracted from the microarrays using Agilent’s DNA microarray scanner and Feature Extraction Software (Agilent Technologies).
Contributor(s) Cui Y, McBride SJ, Boyd WA, Alper S, Freedman JH
Citation(s) 17592649
Submission date Apr 17, 2007
Last update date Dec 06, 2012
Contact name Yuxia Cui
Phone 919-541-2679
Fax 919-541-5737
Organization name NIEHS
Department ETP, DIR
Street address 111 TW Alexander Dr.
City Research Triangle Park
State/province NC
ZIP/Postal code 27709
Country USA
Platforms (1)
GPL2875 Agilent-012795 C. elegans Oligo Microarray G2518A Option 002 (Feature Number version)
Samples (36)
GSM182402 C. elegans_Cd_4h_rep1
GSM182403 C. elegans_Cd_4h_rep2
GSM182404 C. elegans_Cd_4h_rep3
BioProject PRJNA99411

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Supplementary file Size Download File type/resource
GSE7535_RAW.tar 857.4 Mb (http)(custom) TAR (of TIFF, TXT)
Processed data included within Sample table

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