NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM747209 Query DataSets for GSM747209
Status Public on Jun 30, 2012
Title Lung_15mg silica_0 week post-exposure_rep4
Sample type RNA
 
Source name 15mg/m3 silica, 0 week post-exposure, rat 84 lung
Organism Rattus norvegicus
Characteristics strain: CDF Fisher 344
gender: male
age: 3 months
tissue: lung
treatment: 15mg/m3 crystalline silica
post-exposure time: 0 weeks
rat identifier: 84
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 16-hours 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 the RNeasy Fibrous Tissue Mini kit (Qiagen Inc, Valencia, CA) following the protocol provided by the kit manufacturer. The total RNA isolated was digested with RNase-free DNase following the recommendations of the supplier.
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).
 
Hybridization protocol Employing materials and protocols provided by Illumina, Inc. (San Diego, CA,), each labeled cRNA sample was hybridized to the RatRef-12 v1.0 expression beadchip (Illumina, Inc.) for 20 hrs at 58C. 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.
Scan protocol The arrays were scanned with the Illumina BeadStation 500 platform following the protocol provided by the manufacturer (Illumina, Inc., San Diego, CA).
Description T0_L_S(15)_4
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.
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/Bioconductor 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/packages/2.2/bioc/vignettes/lumi/inst/doc/lumi.pdf). Robust spline normalization was used to generate the values in the matrix table. After normalization, Lumi code deletes undetected genes, resulting in a subset of genes detected on the array. A linear model analysis using the '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.
 
Submission date Jun 23, 2011
Last update date Jun 30, 2012
Contact name Rajendran Sellamuthu
E-mail(s) rajsella@indiana.edu
Organization name National Institute for Occupational Safety and Health
Department HELD
Lab Molecular Carcinogenesis
Street address 1095 Willowdale Rd
City Morgantown
State/province WV
ZIP/Postal code 26505
Country USA
 
Platform ID GPL6101
Series (2)
GSE30178 Mechanisms of crystalline silica-induced pulmonary toxicity revealed by global gene expression profiling (rat lungs)
GSE30216 Mechanisms of crystalline silica-induced pulmonary toxicity revealed by global gene expression profiling

Data table header descriptions
ID_REF
VALUE Robust spline-normalized signal intensity computed by the 'lumi' Bioconductor package
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1369537 7.276420513 0.002424242
ILMN_1358051 6.835166754 0.02424242
ILMN_1357910 7.867462167 0
ILMN_1352975 6.793525023 0.04606061
ILMN_1368384 8.869313104 0
ILMN_1376898 6.87308595 0.01333333
ILMN_1368325 7.578119462 0.001212121
ILMN_1353563 8.669733916 0
ILMN_1364273 8.219882929 0
ILMN_1349007 7.803070956 0.001212121
ILMN_1355155 10.34942626 0
ILMN_1362563 6.800449438 0.04
ILMN_1355815 6.797451819 0.04363636
ILMN_1374139 9.184976263 0
ILMN_1650701 8.764098223 0
ILMN_1350564 8.415218392 0
ILMN_1354174 10.10618177 0
ILMN_1356772 6.993626886 0.006060606
ILMN_1368155 8.05177291 0
ILMN_1368329 7.232580106 0.002424242

Total number of rows: 12763

Table truncated, full table size 395 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap