The wild type C. elegans strain (N2) were grown at 20°C on nematode growth medium (NGM), with E. coli OP50 as food source
Extracted molecule
total RNA
Extraction protocol
Total RNA from each group was extracted using TRIzol reagent following manufacturer’s instruction (Invitrogen, USA), purified using RNeasy Mini Kit (Qiagen, USA)
Label
Biotin
Label protocol
Purified total RNA was amplified and labeled with biotinylated nucleotide analog using Affymetrix GeneChip 3’ IVT Express Kit according to the manufacturer’s protocol.
Hybridization protocol
The biotin-labeled amplified RNA (aRNA) was then fragmented before being hybridized onto the genome array. The hybridization controls was used to monitor the hybridization quality, which composed of a mixture of biotinylated and fragmented cRNA of bioB, bioC, bioD and cre prepared in staggered concentrations (1.5, 5, 25, and 100 pM respectively). Using Affymetrix Genechip C. elegans Genome Array, 22 625 transcripts were screened for changes in expression patterns and levels. After 17 hours of hybridization, washing and scanning of the arrays was carried out using GeneChip Hybridization, Wash and Stain Kit (Affymetrix) in GeneChip Fluidics 450 system.
Scan protocol
GeneChips were scanned using the GeneChip 3000 Scanner.
Description
Nematodes after 2-hours induction with 0.3 mM H2O2 at L4 stage
Data processing
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method in Expression Console software (Affymetrix).
