Differential gene expression in the Pancreatic lymph node of Deaf1 knockout mice vs. wild type littermate controls
ABSTRACT: Gene expression in the the pancreatic lymph node of 4, 12, and 30 week old Deaf1-knockout (KO) mice compared to BALB/c littermate controls. Gene expression was measured in the pancreatic lymph nodes of 4 wk old Deaf1 KO mice (2 replicates), 12 wk old Deaf1-KO mice (3 replicates), and 30 wk old Deaf1-KO mice (3 replicates).
Project description:This SuperSeries is composed of the following subset Series: GSE29152: Lymph node stromal cells: Control siRNA treated vs. Eif4g3 siRNA treated GSE29153: Differential gene expression in the Pancreatic lymph node of Deaf1 knockout mice vs. wild type littermate controls Refer to individual Series
Project description: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. 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.
Project description:These experiments were performed to identify differentially expressed genes in the pancreatic lymph nodes of hyperglycemic NOD mice with high levels of destructive insulitis compared to euglycemic mice with lower levels of insulitis. The pancreatic lymph nodes of 16-week-old hyperglycemic and euglycemic NOD mice were isolated and homogenized in Trizol reagent (Invitrogen). Total RNA was extracted from the aqueous phase using the RNeasy mini kit (Qiagen). RNA quality was assessed using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Reagent Kit (Agilent). Total RNA from the PLN of hyperglycemic mice (n=2) were labelled with Cy5 and run individually against a pool of Cy3-labeled total RNA isolated from euglycemic mice (n=2). Microarrays were performed using the Whole Mouse Genome Microarray Kit, 4×44K 2-color arrays (Agilent Technologies).
Project description:Gene expression in the the pancreatic lymph node of 4, 12, and 30 week old Deaf1-knockout (KO) mice compared to BALB/c littermate controls. Overall design: Gene expression was measured in the pancreatic lymph nodes of 4 wk old Deaf1 KO mice (2 replicates), 12 wk old Deaf1-KO mice (3 replicates), and 30 wk old Deaf1-KO mice (3 replicates).
Project description:Normal gene expression in pancreatic lymph nodes compared to inguinal or mesenteric lymph nodes across different strains of mice (BALB/c, FVB, NOD, NOD.B10). Lymph nodes were excised from 12 wk old female mice (5 mice per group), and total RNA was extracted for dual dye microarray analysis.
Project description:We have developed a transgenic mouse model for Epstein-Barr virus-associated Burkitt's lymphoma. Transgenic mice that express LMP2A and MYC in B cells develop spontaneous lymph node tumors at different rates. Tumor onset occurs at approximately 40-60 days in LMP2A/λ-MYC mice and at 100-200 days in λ-MYC mice. This study compared total gene expression in the tumor cells from each genotype, as well as in B cells isolated from 3 week old mice prior to tumor onset. Comparison of total gene expression in tumor cells from LMP2A/λ-MYC and λ-MYC transgenic mice identified a short list of differentially expressed genes. Comparison of gene expression in B cells from the spleens of 3 week old mice, in contrast, identified a 10-fold increase in the number of differentially expressed genes. B cells from the spleens of 3 week old LMP2A/λ-MYC (n=5), λ-MYC (n=5), LMP2A (n=3), and WT (n=3) transgenic mice were purified using magnetic-activated cell sorting (MACS) beads purchased from Miltenyi for CD19 positive selection. Total RNA was isolated from these purified B cells, as well as from cervical lymph node tumor cells that developed in LMP2A/λ-MYC (n=7) and λ-MYC (n=5) transgenic mice using RNeasy RNA extraction kit from QIAGEN. Cervical lymph node tumor cells were >90% positive for the B cell marker B220, and were not further purified. Total gene expression was assessed in each sample, along with heart and brain reference samples using MouseRef-8 v2.0 Expression Bead Chips purchased from Illumina. GeneSpring analysis software was used to analyze the expression data and identify significantly differentially expressed genes (fold change >1.5-fold and false discovery rate< 0.05).
Project description:Gene expression in the islets of diseased NOD mice compared to congenic healthy NOD.B10 mice at various ages, during the progression of NOD disease. Islets were isolated from individual NOD and NOD.B10 mice by collagenase digestion. RNA was extracted using Trizol, combined with the RNeasy micro kit (Qiagen). RNA quality was assessed using the Agilent 2100 Bioanalyzer and the RNA 6000 Pico Reagent Kit (Agilent). Microarrays were performed using the Whole Mouse Genome Microarray Kit, 4×44K 2-color arrays (Agilent Technologies).
Project description:As part of a study of the role of the aryl hydrocarbon receptor (Ahr) in maintenance and senescence of hematopoietic stem cells (HSC), global gene expression profiling was done with HSC isolated from bone marrow restricted conditional Ahr-knockout and AhR floxed mice. HSC from young-adult (8 wk old) cAhR-KO mice had changes in expression of many genes related to HSC maintenance, consistent with the phenotype observed in Ahr-KO mice. Aged cAhR-KO mice (18 months old) also displayed alterations in peripheral white blood cell counts, serial repopulation potential and levels of ROS in bone marrow cells, consistent with previous observations on the role of AhR in the hematopoietic system. 22 samples: 5 young Ahr knockout, 6 old Ahr knockout, 5 young floxed Ahr, 6 old floxed Ahr
Project description:Comparison of the gene expression in the two pancreatic lymph nodes: gastric lymph node (GLN) and pancreatico-duodenal lymph node (PDLN) in NOD mice. The analysis was done in an attempt to explain the preferential homing of bone marrow-derived dendritic cells to the GLN after intravenous injection. GLN and PDLN were excised from 4 individual 12-wk old female NOD mice and RNA was extracted after tissue homogenization in Trizol for processing onto microarray (Agilent 4x44K). Each array corresponds to one single mouse, thus this study comprise 4 biological replicates.
Project description:Normal gene expression in pancreatic lymph nodes compared to inguinal or mesenteric lymph nodes across different strains of mice (BALB/c, FVB, NOD, NOD.B10). Overall design: Lymph nodes were excised from 12 wk old female mice (5 mice per group), and total RNA was extracted for dual dye microarray analysis.