|
| Status |
Public on May 15, 2014 |
| Title |
Parenchyma-sham 4 |
| Sample type |
RNA |
| |
|
| Source name |
Parenchyma-sham
|
| Organism |
Rattus norvegicus |
| Characteristics |
gender: male
tissue: Parenchyma
tissue source: Left Lung
treatment: fresh air
treatment concentration [ug nicotine/l]: 0
treatment duration [days]: 28
daily exposure [hours]: 1
exposure path: nose-only
smoking regimen: --
|
| Treatment protocol |
Animals were exposed to mainstream smoke smoke through nose-only inhalation for 28 days with varying doses (0, 8, 15, 23 ug nicotine/l) and different tobacco products (pMRTP and 3R4F).
|
| Growth protocol |
na
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole tissue for nasal epithelia or laser microdissected (LCM) tissue for bronchi and lung parenchyma was used to extract total RNA using miRNAeasy Mini Kit (Qiagen).
|
| Label |
biotin
|
| Label protocol |
GeneChip(R) 3’ IVT Express Kit (Affymetrix, Santa Clara, USA) with 100 ng RNA.
|
| |
|
| Hybridization protocol |
The biotin-labeled RNA was hybridized on Affymetrix Rat230_2 microarrays. The wash and stain procedures were performed according to Affymetrix protocols (GeneChip(R) Expression Wash, Stain and ScanUser Manual, Affymetrix).
|
| Scan protocol |
Cartridges were scanned using the GeneChip Scanner 3000 (Affymetrix). Scanned image files were visually inspected for artifacts and the generated Cel files was used as input for data analysis. The Affymetrix Command Console Software (AGCC, Affymetrix, Santa Clara, CA) was used to control the fluidics station and the scanner.
|
| Description |
910096-Paren
|
| Data processing |
Data processing was implemented in the R statistical environment. Raw RNA expression data was analyzed using the affy and gcrma packages of the Bioconductor suite of microarray analysis tools available in the R statistical environment. GC Robust Microarray Analysis (GCRMA) (including background correction and quantile normalization) was used to generate probe set expression values.
|
| |
|
| Submission date |
Aug 27, 2013 |
| Last update date |
May 15, 2014 |
| Contact name |
Sam Ansari |
| E-mail(s) |
sam.ansari@pmi.com
|
| Organization name |
Philip Morris Products SA
|
| Department |
Research & Development
|
| Lab |
Biological Systems Research
|
| Street address |
Quai Jeanrenaud 5
|
| City |
Neuchatel |
| State/province |
Neuchatel |
| ZIP/Postal code |
2000 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL1355 |
| Series (1) |
| GSE50254 |
Integration of toxicological end points with molecular measurements in a 28-day rat repeated dose inhalation study with cigarette smoke provides mechanistic understanding of smoke impact |
|
