cell line: AG1522 cell type: skin fibroblast treatment: 5 cGy followed by 2 Gy X-ray radiation time: 12 h
Treatment protocol
The gene profiles for the 5 cGy groups i.e., those subjected to 5 cGy irradiation at different time points after irradiation, including 0 (baseline), 3, 6, 12 and 24 h, were examined.For the 2 Gy groups, i.e., those subjected to 2 Gy irradiation, at 0, 3, 6, 12 and 24 h after irradiation were examined.The gene profiles for the (5 cGy + 2 Gy) groups exposed to 5 cGy (priming dose) and then followed by 2 Gy (challenge dose), the time points 0, 3, 6, 12, 24 h after application of the challenging dose were examined.
Growth protocol
Human skin fibroblast AG 1522 cells were cultured in modified α-MEM (Hyclone, Logan, US) supplemented with 20% fetal bovine serum (FBS) (Hyclone, Logan, US), 1% penicillin/streptomycin, 1% glutamine and 1% non-essential amino acids mix (Sigma-Aldrich, St. Louis, US). All cultures were grown in a humidified 5% CO2 atmosphere at 37℃. Prior to treatment, the confluence of cells obatined to 100%.
Extracted molecule
total RNA
Extraction protocol
Trizol extraction of total RNA was performed according to the manufacturer's instructions.Qualified total RNA was further purified using the RNeasy micro kit (QIAGEN, GmBH, Germany) and genomic contamination was removed by RNase-Free DNase Set (QIAGEN, GmBH, Germany).
Label
biotin
Label protocol
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.
Hybridization protocol
Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45℃ on PrimeView Human Chip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol
Scanning was performed on a seventh-generation GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA, US). Affymetrix GCOS software was used for image analysis to generate raw intensity data.
Description
Gene expression data from AG 1522 human fibroblasts 12 h after 5 cGy + 2 Gy X-ray radiation (12 h interval). AG_5p2_12h-3
Data processing
The data were analyzed with Bioconductor.Normalization was performed with the RMA algorithm which included the global background adjustment and quantile normalization.
