Project name: Mus musculus

Description: We hypothesized that homeostatic interactions between naïve CD4+ T cells and resident cells in the liver generates signals that modulate gene expression in this organ. To test this hypothesis, we identified genes that are regulated by the presence of naïve CD4+ T cells by using a whole genome microarray to compare transcript levels in liver tissue from non-infected RAG-1-/-, OT-II/RAG-1-/- and wild type mice (Fig. 3). Using this approach, we identified 175 genes that were differentially expressed only in the presence of naïve CD4+ T cells.Keywords: Genotype comparisonOverall design: Livers from naïve female wild type C57BL/6, RAG-/-, and OT-II/RAG-/- (N=9 for each genotype) mice were pooled into groups of three and prepared for cDNA microarray analysis. Briefly, RNA was isolated via RNAzol (Tel-Test, Friendswood, TX) and the RNeasy protocol (Qiagen) and analyzed for purity and concentration on a NanoDrop® ND-1000 Spectrophotometer (Wilmington, DE). cDNA was prepared from two 30 µg aliquots of each pooled sample and labeled with either Cy3 or Cy5 fluorescent probes. One 30 µg aliquot from each pool was used to create a background control pool, while the second aliquot was used as the comparative sample. For further isolation and labeling protocol details please refer to http://www.niaid.nih.gov/dir/services/rtb/microarray/protocols.asp. Samples were hybridized as described by Schaupp (9) to Mmbe custom arrays manufactured by the NIAID Microarray Facility. Further information about these arrays can be found at http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL1057. Hybridizations were performed in triplicate. Images were scanned by GenePix4000B Scanner (Axon Instruments/Molecular Devices, Sunnyvale, CA) and analyzed using the mAdb program (http://madb.niaid.nih.gov/). Signals were calculated as mean intensity – median background. Data were analyzed using Significance Analysis of Microarrays (SAM), version 2.11 (Stanford University) and student’s T tests (EXCEL, with P values <0.05 considered significant) to identify only those genes that exhibited differential expression in RAG-1-/- liver tissue compared to both OT-II/RAG-1-/- and wild type liver tissue (i.e. genes differentially expressed in RAG-1-/- liver tissue compared to either OT-II/RAG-1-/- or wild type alone were not considered specific to the presence of naïve CD4+ T cells).

Data type: Transcriptome or Gene expression

Sample scope: Multiisolate

Relevance: ModelOrganism

Release date: 2007-12-01

Last updated: 2007-06-30