|
| Status |
Public on Jan 19, 2008 |
| Title |
SeV 3483 |
| Sample type |
RNA |
| |
|
| Source name |
Sendai virus infected mouse tracheal epithelial cells.
|
| Organism |
Mus musculus |
| Characteristics |
Strain: C57BL/6J
Gender: Male
Tissue: primary culture tracheal epithelial cells
|
| Treatment protocol |
Sendai virus (SeV), strain 52, was obtained from American Type Culture Collection and stored at -70°C. Cultures were inoculated with SeV or an equivalent amount of UV-inactivated SeV (SeV-UV) in the apical compartment for 1 h at 37 °C, then removed by washing. RNA was collected 24 hours after inoculation.
|
| Growth protocol |
Primary-culture mouse tracheal epithelial cells (mTECs) were established on Transwell membranes using air-liquid interface (ALI) conditions as described previously (Tyner et al, 2006).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from mTEC cultures using the Micro RNA Isolation kit (Stratagene) and converted to Poly(A)+ RNA.
|
| Label |
biotin
|
| Label protocol |
Poly(A)+ RNA was amplified using RiboAmp (Arcturus, Mountain View, CA), and then labelled with biotin using the BioArray High Yield RNA Transcript Labeling Kit (Enzo, Farmingdale, NY)
|
| |
|
| Hybridization protocol |
Samples were hybridized in duplicate to gene chip U74Av2 (Affymetrix, Santa Clara, CA) according to the manufacturer’s protocol.
|
| Scan protocol |
Chips were scanned, and hybridization data were acquired using Affymetrix MicroArray Suite (MAS) 5.0 software.
|
| Description |
epithelial cell response to sendai virus infection
|
| Data processing |
Microarray normalization and statistical analysis were carried out using packages from the Bioconductor project (Gentleman RC et al, 2004, ver 2.0), executed in the R programming environment. Data was normalized using the empirical Bayes version of the GCRMA algorithm as implemented in the GCRMA package (Wu Z et al, 2004). Differential expression was assessed by using linear models and empirical Bayes moderated F statistics as implemented in the LIMMA package (Smyth GK, 2004). Differences in gene expression were considered significant if the P values were <0.05 after adjustment for multiple testing (Benjamini & Hochberg, 1995), and thus, false discovery rate was controlled to be <5%. Visualization and plotting were performed using Spotfire DecisionSite for Functional Genomics (Spotfire, Somerville, MA).
|
| |
|
| Submission date |
Jan 18, 2008 |
| Last update date |
Jan 18, 2008 |
| Contact name |
Anand Champak Patel |
| E-mail(s) |
acpatelmd@gmail.com
|
| Organization name |
Washington University School of Medicine
|
| Department |
Pulmonary/Critical Care Medicine
|
| Lab |
Patel
|
| Street address |
Campus Box 8116, 660 S. Euclid Ave.
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL81 |
| Series (1) |
| GSE10211 |
Airway Epithelial Cell Response to Sendai virus infection |
|
