Microarray-based Transcriptomics of C. elegans

After the 24-h exposure, all 400 worms per well were collected into a cryogenic vial and spun at 1150×g for 2.5 min. Supernatant was removed and the vial were flash frozen in liquid nitrogen and stored at − 80 °C. Total RNA was extracted from each vial using RNeasy mini kits (Qiagen, Valencia, CA) and treated as one biological replicate. Four of the five replicates (total RNA samples) per treatment were chosen for further microarray hybridization. One hundred ng of total RNA was first reverse-transcribed into cDNA, followed by cDNA labeling using Low Input Quick Amp Labeling Kits (Agilent, Palo Alto, CA) in the presence of cyanine 3-CTP dye. The labeled cDNA was hybridized to the C. elegans-specific 44 K-olig array (one sample/array) at 65 °C for 17 h using Agilent’s Gene Expression Hybridization Kits [39 (link)]. A total of 48 samples (3 chemicals × 4 treatments per chemical × 4 replicates per treatment) were randomly assigned and hybridized to six 8 × 60 K-array slides containing 44 K oligonucleotide probes per array.