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| Status |
Public on May 19, 2010 |
| Title |
SPL tissue- and age-specific changes in gene expression during disease induction and progression in NOD mice. |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
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| Summary |
41K whole genome oligo-microarrays (Agilent Technologies) were used to characterize age-dependent changes in gene expression in spleen (SPL) obtained from up to 5 individual NOD mice at 6 different time points (10 days (n=5), and 4 weeks (n=5), 8 weeks (n=3), 12 weeks (n=5), 16 weeks (n=4), and 20 weeks of age (n=5)), compared to NOD.B10 tissue controls. "Milestone Genes" are genes whose expression was significantly changed (approximately 3 fold) as the result of splicing or changes in transcript level. Milestone Genes were identified among genes within type one diabetes (T1D) susceptibility regions (Idd). Milestone Genes showing uniform patterns of changes in expression at various time points were identified. Potential T1D candidate genes were identified among Milestone Genes within Idd regions and/or hierarchical clusters. These studies identified tissue- and age-specific changes in gene expression that may play an important role in the inductive or destructive events of T1D.
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| Overall design |
NOD/LtJ (NOD), NOD.B10Sn-H2b/J (NOD.B10) female mice of multiple ages were used for this study.
Six Groups of NOD mice were sacrificed at 10 days, and 4, 8, 12, 16, and 20 weeks of age and spleen (SPL) were removed and prepared for mRNA analysis. Two Groups of 10 NOD.B10 mice [10 days (n=10) + 20 weeks of age (n=10)] were used as a tissue specific control. Gene (mRNA) expression was analyzed using the 41K Whole Mouse Genome Oligo Microarray Kit (Agilent Technologies), and gene expression data are processed (cy3: NOD, cy5: NOD.B10) and reported as normalized expression ratios: Log 10 (NOD processed signal / NOD.B10 processed signal) (Log ratio).
10days of age; SPL_10d (n=5), 4 weeks of age; SPL_4w (n=5), 8 weeks of age; SPL_8w (n=3), 12 weeks of age; SPL_12w (n=5), 16 weeks of age; SPL_16w (n=4), 20 weeks of age; SPL_20w (n=5)
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| Web link |
http://fathmanlab.stanford.edu/roadmap_study_design.html
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| Contributor(s) |
Kodama K, Butte AJ, Creusot RJ, Su L, Sheng D, Hartnett M, Iwai H, Soares LR, Fathman G |
| Citation(s) |
18801706 |
| Submission date |
May 17, 2010 |
| Last update date |
Dec 06, 2012 |
| Contact name |
Keiichi Kodama |
| E-mail(s) |
kkodama@stanford.edu
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| Organization name |
Stanford Univeristy School of Medicine
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| Department |
Department of Medicine, Division of Immunology & Rheumatology
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| Lab |
Fathman
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| Street address |
269 Campus Drive, Room 2225
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305-5166 |
| Country |
USA |
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| Platforms (1) |
| GPL2872 |
Agilent-012694 Whole Mouse Genome G4122A (Feature Number version) |
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| Samples (27)
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| Relations |
| BioProject |
PRJNA126891 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE21884_RAW.tar |
334.2 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
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