zebrafish embryos were collected from three wild type breeding pairs, pooled, and allowed to develop for 24 hours. One group of ~50 embryos was withdrawn to serve as the non-irradiated control (Group A). To investigate the long-term response, two other groups of ~50 embryos each were withdrawn and irradiated with 0.1 Gy (Group B) or 1.0 Gy (Group C) of 137Cs γ-rays (Model 68A irradiator, J. L. Shepherd & Associates, San Fernando, CA). At 16 weeks post-fertilization, six males from each group were randomly selected, anesthetized with MS-222 (ethyl 3-aminobenzoate methanesulfonate salt; Sigma–Aldrich, St. Louis, MO), sacrificed, sex verified, and dissected. Livers were removed and rapidly frozen in TRIzol Reagent (Life Technologies, Grand Island, NY). In addition, 12 males from Group A were randomly selected and used to establish the acute response groups. These were subjected to whole body irradiation at 0.1 Gy (Group D) or 1.0 Gy (Group E) and sacrificed for analysis at 4 hours post-irradiation
Growth protocol
Embryos in all groups were allowed to grow and develop at 28 ºC using standard maintenance protocols
Extracted molecule
total RNA
Extraction protocol
Total RNA extraction, cDNA synthesis, and synthesis and labeling of antisense RNA was performed as recommended by Affymetrix using Life Technologies kits.
Label
biotin
Label protocol
Total RNA extraction, cDNA synthesis, and synthesis and labeling of antisense RNA was performed as recommended by Affymetrix using Life Technologies kits.
Hybridization protocol
Total RNA extraction, cDNA synthesis, and synthesis and labeling of antisense RNA was performed as recommended by Affymetrix using Life Technologies kits.
Scan protocol
standard Affymetrix protocol
Description
livers of 16 week old adults, irradiated as embryos
Data processing
The data were analyzed using Bioconductor, using quantile normalization and RMA for background subtraction.
