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Sample GSM89788 Query DataSets for GSM89788
Status Public on Mar 30, 2006
Title HVB_253_F2_B: F2 mouse # 253 , Low Goblet Cell Metaplasia, High 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 (TrizolĀ®, 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).
 
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 GPL82
Series (1)
GSE3925 Virus Induced Airway Hyperreactivity and Goblet Cell Metaplasia Phenotypic Extremes (CB6F2/J)

Data table header descriptions
ID_REF Affymetrix U74Bv2 probe ID
VALUE normalized intensity by gcRMA

Data table
ID_REF VALUE
104769_at 3.443720348
104770_at 2.984042162
104771_at 5.612783822
104772_at 5.435593202
104773_at 3.887719935
104774_at 4.504255852
104775_at 6.110381633
104776_at 2.786471988
104777_at 3.928339855
104778_at 2.385522816
104779_at 1.256118492
104780_at 3.543037776
104781_at 3.330160785
104782_at 8.75957637
104783_at 6.393200817
104784_at 5.086306341
104785_at 3.051242895
104786_at 4.46822372
104787_at 3.305297959
104788_at 1.688114486

Total number of rows: 12477

Table truncated, full table size 270 Kbytes.




Supplementary data files not provided

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