Transcriptomics

Dataset Information

3

Transcription profiling of C. elegans treated with oxidative stress vs. controls


ABSTRACT: Oxidative stress may play a role in normal aging. SKN-1 is a transcription factor necessary for intestine development in Caenorhabditis elegans, which also regulates the response to oxidative stress post-embryonically. Using DNA microarrays, we found that oxidative stress induces the antioxidant response, the heat shock response, and detoxification genes, while the expression of genes involved in homeostasis, development, and reproduction were decreased. Both up-regulated and down-regulated genes can be wholly, partially, or not at all dependent on SKN-1 action. However, induction of the heat shock response by oxidative stress was not affected by SKN-1 removal. Experiment Overall Design: TJ1060 was grown at 16 C. Eggs were collected by hypochlorite, hatched overnight at 20 C (Emmons, 1979 #52) and first-stage larvae (L1’s) were placed onto 2 % peptone plates (1.7 % agar, 20 g/l peptone, 25 mM NaCl, 50 mM KH2PO4 pH 6.0, 5 µg/ml cholesterol, 1 mM CaCl2, 1 mM MgSO4) at 25 C. Sterile 3 day old young adult animals on peptone plates were treated with 99 % O2 at 40 PSI for 6 hours at 20 C in a hyperbaric O2 chamber. Half of the worms were untreated and served as a control population. A small plate of strain CL2166 [dvIs19 pAF15(gst-4::GFP::NLS)] was used as an indicator strain and checked for GFP induction in both control and experimental conditions. Worms were harvested by washing off plates with S-basal and quick frozen in liquid nitrogen. Total RNA was prepared using TRIZOL reagent and standard protocols and cleaned up on Qiagen RNeasy columns. The Affymetrix labeling kit was used to prepare labeled cRNA as a target for the Affymetrix GeneChip® C.elegans Genome Array. Gene chip hybridization and scanning were done at Genome Explorations (Memphis, MN) and the University of Colorado at Boulder Gene Chip Core Facility (Boulder, CO).

INSTRUMENT(S): 418 [Affymetrix]

ORGANISM(S): Caenorhabditis elegans  

SUBMITTER: Sang-Kyu Park  

PROVIDER: E-GEOD-9301 | ArrayExpress | 2008-06-16

SECONDARY ACCESSION(S): GSE9301PRJNA102949

REPOSITORIES: GEO, ArrayExpress

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