tissue: right lung, lobe 1 strain: ICR age: 5 to 6 weeks old treatment group: 0.5mg SWCNTs treated on day 1
Treatment protocol
The intratracheal instillation procedure: anesthetized with pentobarbital (80 mg•kg-1, Sigma, St. Louis, MO, USA; intraperitoneally), individual mice were secured on an inclined plastic platform. The trachea was exposed by a 1 cm incision in the ventral neck skin for instillation of Pluronic F-68 (PF68, solvent control) or the SWCNTs [0.5 mg per mouse in a 50 µl 0.1% Pluronic F-68 aliquot]; SWCNTs (SE grade, purity > 95%) was purchased from CarboLex, Inc, (McCarty, Court, Lexington).
Growth protocol
Adult male ICR mice (5~6 weeks old), were purchased from the laboratory animal center of National Taiwan University College of Medicine (Taipei, Taiwan). Mice were cared and used humanely according to the Guide for the Care and Use of Laboratory Animals as adopted and promulgated by the National Health Research Institutes (NHRI, Taiwan).
Extracted molecule
total RNA
Extraction protocol
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label
biotin
Label protocol
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)(Santa Clara, CA, USA, http://www.affymetrix.com).
Hybridization protocol
Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Genome 430A plus 2.0 GeneChip on Affymetrix Hybridization Oven 645, 60 RPM, then washed and stained in the Affymetrix GeneChip Fluidics Station 450.
Scan protocol
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
Description
Gene expression data from mice lung tissues treated with 0.5 mg SWCNTs in acute response phase, day 1).
Data processing
The expression data were analyzed by the SAS JMP Genomics software (Version 4.0; SAS Institute Inc., Cary, NC). Affymetrix CEL files were transformed by RMA algorithm, imported at the probe level and log2 transformed, and each probe set was summarized using the median of the corresponding probes. Each array was normalized by Quantile Normalization.
