strain: Fisher (CDF) 344 gender: Male age: Approximately 3 month old tissue: Lung stress: silica time: 44 week post-exposure
Treatment protocol
Rats were exposed to air (control) or crystalline silica by inhalation (15 mg/m3, 6 hours/day, 5 days). Rats were sacrificed at 44 weeks following the last silica exposure.
Growth protocol
Rats were housed in the animal facility at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV. The animals were kept under controlled lighting (12-hour light-dark cycle), temperature (72 ± 50 F), and humidity (50 ± 20%) with free access to food and water.
Extracted molecule
total RNA
Extraction protocol
Total RNA was isolated from the lung samples using RNeasy Fibrous Tissue Mini Kit (Qiagen, Inc, Valencia, CA) with on-column DNA digestion following the manufacturer's instructions.
Label
Biotin
Label protocol
Biotin-labeled cRNA was generated from 375 ng RNA samples each by employing the Illumina TotalPrep RNA Amplification Kit (Ambion, Inc, Austin, TX). The labeling of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV
Hybridization protocol
Employing materials and protocols provided by Illumina, Inc (San Diego, CA,), each labeled cRNA sample was hybridized to RatRef-12 v1.0 expression beadchip (Illumina, Inc,) for 20 hrs at 580C. Following hybridization, microarrays were washed to remove unbound and non-specifically hybridized target molecules and stained with Cy3-streptavidin conjugate (Illumina, Inc,). This was followed by a non-stringent washing to remove unbound conjugate. The hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV
Scan protocol
The arrays were scanned with the Illumina BeadStation 500 platform, following the protocol provided by the manufacturer (Illumina, Inc). Scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.
Description
Sample name: T44_L_S(15)_5
Data processing
Array data were extracted using Illumina's BeadStudio software (Framework version 3.0.19.0). Normalization and statistical analysis of the expression data were carried out in R/Bioconducter using the ‘lumi’ and ‘limma’ packages. The ‘lumi’ Bioconductor package covered the data input, quality control, force positive background correction, variance stabilization, normalization and gene annotation (http://bioconductor.org/packagees/2.2/ bioc/vignettes/lumi/inst/doc/lumi.pdf). Robust spline normalization was used to generate the values in the data table. After normalization, Lumi code deletes genes undetected (detection p-value, >0.01) and resulting in a subset of genes detected (detection p-value, <0.01) on the array. A linear model analysis using ‘limma’ package in R was conducted to identify differentially expressed genes. p values were calculated and log fold changes were converted to standard fold changes. Resulting raw p-values were corrected for false discovery rate using the Benjamini-Hochberg method.
