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| Status |
Public on Jul 15, 2009 |
| Title |
Gene expression in the pancreatic lymph node of Deaf1 knock out mice vs. BALB/c controls |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
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| Summary |
A microarray study performed in the pancreatic lymph nodes of Deaf1 knock-out and BALB/c control mice to identify genes that are regulated by the transcriptional regulator Deaf1. These experiments constitute a portion of the study described below:
Abstract:
Type 1diabetes (T1D) can result from a breakdown in peripheral tolerance which is controlled by peripheral tissue antigen (PTA) expression in lymph nodes. Here, we identified a transcriptional regulator, deformed epidermal autoregulatory factor 1 (Deaf1), which regulates the expression of various PTAs in the pancreatic lymph node (PLN). We found, by microarray, that Deaf1 controls the expression of ~600 genes in the PLN. In the non-obese diabetic (NOD) mouse model of T1D, we identified a wild-type form of Deaf1 (DF1) and a truncated alternatively spliced variant (DF1-VAR1) that hetero-dimerizes with and decreases the transcriptional activity of DF1. The expression of DF1 correlates with the expression of various pancreatic PTAs such as insulin, and during the onset of destructive insulitis in NOD mice, DF1 expression is downregulated, while the DF1-VAR1 expression is upregulated in the PLN. A reduction in DF1-controlled PTA expression in the PLN, leading to decreased peripheral tolerance, could underlie the pathogenesis of NOD disease.
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| Overall design |
Deaf1-KO mice (4 wk old) and age-matched BALB/c control mice were sacrificed, and the PLN were removed and immediately homogenized in Trizol Reagent. RNA was extracted in Trizol and then purified using the RNeasy kit (Qiagen). RNA quality was assessed using the Agilent RNA 6000 Nano Reagents, RNA Nano chips, and the Agilent 2100 bioanalyzer (Agilent Technologies), according to manufacturer’s instructions. Control and Deaf1-KO mouse RNA was amplified, labeled with Cy3 and Cy5, respectively, and combined with spike A and spike B mix, respectively, using the Agilent low RNA input fluorescence linear amplification kit (Agilent Technologies). The amplified cRNA was purified using the RNeasy kit (Qiagen), and specific activity was determined with the NanoDrop 1000 spectrophotometer (Thermo Scientific). Samples were prepared with the gene expression hybridization kit (Agilent Technologies) and two color microarrays were performed using the whole mouse genome (4x44K) Oligo microarray kit, according to manufacturer’s instructions. Microarray chips were washed and scanned using the DNA microarray scanner (Agilent Technologies). Data was processed with Feature Extraction Software (Agilent Technologies), and analyzed using GeneSpring GX 7.3 Software (Agilent Technologies). This submission shows the data obtained from two individual Deaf1 knockout mice measured against a pool of 4 BALB/c control mice.
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| Contributor(s) |
Yip L, Creusot RJ, Su L, Sheng D, Chang P, Czesak M, Albert PR, Collier A, Turley SJ, Fathman C |
| Citation(s) |
19668219 |
| Submission date |
Oct 11, 2008 |
| Last update date |
Jan 12, 2017 |
| Contact name |
Linda Yip |
| Organization name |
Stanford University
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| Department |
Medicine
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| Lab |
C.G. Fathman
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| Street address |
269 Campus Drive West, CCSR Building Rm. 2240
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platforms (1) |
| GPL7202 |
Agilent-014868 Whole Mouse Genome Microarray 4x44K G4122F (Probe Name version) |
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| Samples (2) |
| GSM330311 |
Gene expression in the pancreatic lymph node of Deaf1 knock out mice vs. BALB/c controls-sample 1 |
| GSM330312 |
Gene expression in the pancreatic lymph node of Deaf1 knock out mice vs. BALB/c controls-sample 2 |
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| Relations |
| BioProject |
PRJNA109629 |
| Supplementary data files not provided |
| Processed data included within Sample table |
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