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Sample GSM665729 Query DataSets for GSM665729
Status Public on Dec 02, 2011
Title Blood_15mg silica, 8 week post-exposure_rep6
Sample type RNA
 
Source name 15mg/m3 silica, 8 week post-exposure rat 22 blood
Organism Rattus norvegicus
Characteristics strain: CDF Fisher 344
gender: male
age: 3 mo
tissue: blood
treatment: 15mg silica
time: 8 week post-exposure
Treatment protocol Rats were exposed to air (control) or crystalline silica by inhalation (1, 2, or 15 mg/m3, 6 hours/day, 5 days). Rats exposed to 1 or 2 mg/m3, 6 hours/day, 5 days and the corresponding control were sacrificed at 16-hours following the last silica exposure. Rats exposed to 15 mg/m3, 6 hours/day, 5 days and corresponding controls were sacrificed at post-exposure time intervals of 0, 1, 2, 4, 8, and 16 weeks.
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 blood samples using Mouse RibopureTM Blood isolation kit (Ambion Inc, Austin, TX) following the protocol provided by the kit manufacturer. The total RNA isolated was digested with RNase-free DNase and further purified using RNeasy Mini kit (Qiagen Inc, Valencia, CA) following the recommendations of the supplier. The globin mRNA present in abundance in the blood RNA samples was depleted using the GlobinclearTM – Mouse/Rat globin mRNA removal kit (Ambion Inc, Austin, TX).
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 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.
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 The labeling and hybridization of microarray were performed at 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 Feb 02, 2011
Last update date Dec 02, 2011
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 (1)
GSE27023 Blood gene expression profile of control and crystalline silica exposed rats

Data table header descriptions
ID_REF
VALUE Robust spline-normalized signal intensity computed by the 'lumi' Bioconductor package
T8-S(15)-6.Detection Pval

Data table
ID_REF VALUE T8-S(15)-6.Detection Pval
ILMN_1369537 11.81056658 0
ILMN_1358051 6.765700138 0.03272727
ILMN_1361746 6.58423917 0.1575758
ILMN_1351370 6.517356784 0.2569697
ILMN_1357910 6.810061839 0.02666667
ILMN_1352975 6.417644823 0.569697
ILMN_1368384 6.303128218 0.9393939
ILMN_1355285 6.701620725 0.05333333
ILMN_1376898 6.674664211 0.07151515
ILMN_1368325 7.306965939 0.006060606
ILMN_1353563 8.639365114 0
ILMN_1348794 6.300173775 0.9442424
ILMN_1364273 7.181930933 0.006060606
ILMN_1369433 6.555889037 0.2012121
ILMN_1349007 7.831026487 0.002424242
ILMN_1374156 6.667700396 0.07393939
ILMN_1360232 6.273695176 0.9721212
ILMN_1355155 8.733405257 0
ILMN_1362563 6.621561335 0.1163636
ILMN_1355815 7.171622539 0.006060606

Total number of rows: 21792

Table truncated, full table size 728 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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