Differential gene expression in the Pancreatic lymph node of Deaf1 knockout mice vs. wild type littermate controls
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE29153 | GEO | 2011/09/01
SECONDARY ACCESSION(S): PRJNA142985
REPOSITORIES: GEO
Similar Datasets
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. 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).
2011-08-31 | E-GEOD-29153 | biostudies-arrayexpress
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
2011-08-31 | E-GEOD-29167 | biostudies-arrayexpress
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.
2009-07-15 | GSE13163 | GEO
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 manufacturerâs 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 manufacturerâs 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.
2010-04-08 | E-GEOD-13163 | biostudies-arrayexpress
Project description:To determine the different gene signatures between B lymphocytes from tumor draining lymph node (DLN) and normal lymph node (NLN), we have employed gene microarray as a discovery platform to identify gene signatures of tumor-educated B cells in DLN from tumor-bearing mice, taking NLN from normal mice as a control. We subcutaneously inoculated Balb/c mice with breast cancer cell line 4T1. Two weeks later, DLN was harvest and B cells were purified as descript in “treatment protocol”. From gene microarray, we found that B cells in DLN showed quite different transcript profiles from that in NLN.
2018-05-01 | GSE81146 | GEO
Project description:Purpose: The objective was to identify genes regulted by RANK signalling in lymph node lymphatic endothelial cells Method: Lymphatic endothelial cells were FACS sorted from peripheral lymph nodes of mice deficient for stromal RANKL (Ccl19 Cre Rankl flox/flox) versus littermate controls (Rankl flox/flox) and processed for bulk RNA sequencing Results: Upregulated and downregulated genes were identified
2019-06-01 | GSE129315 | GEO
Project description:Expression data from 4T1 subclones derived from mammary fat pad tumors (MFP), axillary lymph node tumors (AxLN), and axillary lymph node-derived lung metastases (AxLN-LuM). In parallel, expression data, in the same subclones, of tail vein-derived (TV) lung metastases. The mechanism of how lymph node metastases seed distant metastases is unknown. We used the 4T1 breast cancer cell line, which is an immune competent model of triple negative breast cancer and spontaneously metastasizes in balb/c mice. 4T1-GFP/fLuc cells were injected into MFP to form tumors and 4T1-mCherry/rLuc cells were injected into axillary lymph nodes to form tumors and then allowed to metastasize to lung. TV cells were allowed to metastasize in the lung. Cells were harvested at different time intervals after the injection. Tumors were extracted, dissociated, and then expanded in vitro to obtain MFP, AxLN, AxLN-LuM and TV-LuM subclones isolated after different time lags with respect to the injection.
2019-08-20 | GSE136031 | GEO
Project description:Spleen and lymph node dendritic cells have a differential capacity do induce and retain iTreg cells. Therefore we performed a comparative analysis of the dendritic cells derived from these two compartments to identify the responsible genes CD11c+ conventional dendritic cells were facs sorted from spleens and lymph nodes of BALB/c animals for RNA extraction and hybridization on Affymetreix microarray
2012-06-29 | E-GEOD-39022 | biostudies-arrayexpress
Project description:In this study we focussed our investigations on ECM remodelling by FRCs during lymph node (LN) expansion, and the interconnection between the cellular and ECM components of the conduit network. We demonstrate a loss of ECM components of the conduit during acute LN expansion
2021-05-11 | PXD015816 | Pride