|
| Status |
Public on Mar 30, 2006 |
| Title |
HVB_54_F2_C: F2 mouse # 54 , Low Goblet Cell Metaplasia, Low Airway Hyperreactivity |
| Sample type |
RNA |
| |
|
| Source name |
whole lung
|
| Organism |
Mus musculus |
| Characteristics |
whole lung, 21 days post-Sendai infection, CB6F2/J
|
| Biomaterial provider |
Jeffrey D. Morton
|
| Treatment protocol |
F1-hybrid CB6F1/J mice were obtained from Jackson Laboratory. F1-hybrid mice were bred to generate an F2 intercross population (CB6F2/J). Mice were inoculated intranasally with Sendai virus (2e5 PFU), and airway hyperreactivity was assessed 21 days post infection as previously described (Walter et al, 2002), after which mice were sacrificed and lungs were harvested, right for RNA, left for histology and analysis of goblet cell metaplasia.
|
| Growth protocol |
Mice were maintained under pathogen-free conditions, and all study protocols were approved by the Washington University Animal Studies Committee.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mice were sacrificed 21 days post-infection with Sendai virus. Lungs were flash frozen liquid nitrogen, and subsequently, total RNA was isolated by the acid guanidinium thiocyanate-phenol-chloroform extraction method (Trizol®, Invitrogen, Carlsbad, CA).
|
| Label |
biotin
|
| Label protocol |
Second-strand cDNA synthesis, was performed using a T7-promoter coupled oligo(d)T primer (GeneChip T7-Oligo(d)T Promoter Primer Kit, Affymetrix, Santa Clara, CA), after which an in vitro transcription (IVT) reaction was performed using an Enzo BioArray High Yield RNA transcript labeling kit (Affymetrix).
|
| |
|
| Hybridization protocol |
standard Affymetrix procedures
|
| Scan protocol |
standard Affymetrix procedures
|
| Description |
mouse whole lung gene expression, 21 days post-Sendai virus infection, CB6F2/J extreme cohorts
|
| Data processing |
Gene expression levels were assessed using oligonucleotide microarrays (Affymetrix gene chip MG U74v2) hybridized to labeled cRNA as described previously (Rozzo S et al, 2001). Differential expression was analyzed by GeneChip 3.1 software (Affymetrix) and was assessed by pairwise comparisons of samples from the 4 extreme cohorts of CB6F2/J mice. Criteria for differential expression required increases or decreases in 12 of the 16 possible pairwise comparisons. Subsequently microarrays were normalized using the GC-RMA algorithm as implemented in Bioconductor (Wu Z et al, 2004, Gentleman RC et al, 2004).
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| |
|
| Submission date |
Dec 28, 2005 |
| Last update date |
Mar 30, 2006 |
| 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 |
GPL83 |
| Series (1) |
| GSE3925 |
Virus Induced Airway Hyperreactivity and Goblet Cell Metaplasia Phenotypic Extremes (CB6F2/J) |
|
