|
| Status |
Public on Jan 01, 2012 |
| Title |
lung_silica_1 |
| Sample type |
RNA |
| |
|
| Source name |
lung, chronically exposed to silica
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Lung
strain: Lewis
treatment: exposed to silica
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Lung tissues were homogenized in the presence of TRI reagent (MRC Molecular Research Center, Cincinnati, OH). Total RNA was isolated using the 1-bromo-3-chloropropane (BCP) phase separation reagent (MRC Molecular Research Center). RNA was precipitated by 2-propanol and washed with 75% ethanol.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA was synthesized by in vitro transcription using the GeneChip IVT Labeling kit (Affymetrix).
|
| |
|
| Hybridization protocol |
Biotin-labeled cRNA was purified (GeneChip Sample Cleanup Module, Affymetrix), and 20 mg of the labeled cRNA was fragmented. The cRNA and fragmented cRNA quality was assessed by the Agilent 2100 Bioanalyzer (Agilent; Foster City, CA) and the RNA 6000 Nano LabChip kit (Agilent). The labeled fragmented cRNA was hybridized to Affymetrix GeneChip Rat 230 2.0 arrays for 16 h at 45oC following the Affymetrix protocol specific to this array type. Washing and staining were performed on the Affymetrix fluidics (450) station according to the antibody amplification protocol (Fluidics script: EukGE-WS2v5).
|
| Scan protocol |
The Gene Chips were scanned using the GeneChip Scanner 3000 (Affymetrix).
|
| Data processing |
The analysis was performed with GeneSpring software package (Agilent Technologies, Santa Clara, CA). All samples were subject to per-chip normalization. Data were filtered twice, a fold change filter (2 fold up or down), and the Statistical Analysis of Microarray software (http://www-stat.stanford.edu/~tibs/SAM/), to find all genes with a < 10% false positive q-score.
|
| |
|
| Submission date |
May 06, 2011 |
| Last update date |
Jan 01, 2012 |
| Contact name |
Raymond J Langley |
| E-mail(s) |
rlangley@lrri.org
|
| Phone |
505-348-9614
|
| Organization name |
LRRI
|
| Department |
immunology
|
| Lab |
324
|
| Street address |
2425 Ridgecrest Dr
|
| City |
Albuquerque |
| State/province |
New Mexico |
| ZIP/Postal code |
87108 |
| Country |
USA |
| |
|
| Platform ID |
GPL1355 |
| Series (1) |
| GSE29110 |
Fibrogenic and redox-related but not proinflammatory genes are upregulated in lewis rat model of chronic silicosis |
|
