Unknown,Transcriptomics,Genomics,Proteomics

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Compare gene expression profiles of TCR transgenic CD4+ T helper type 1 (Th1) vs. type 17 (Th17) cells optimally stimulated by antigen and differentiated under Th1 or Th17 conditions.

ABSTRACT: The comparison of Th1 vs. Th17 cell expression profile has been plagued by 1) rarely use of physiologically relevant antigen-driven T helper cell differentiation; and 2) cell lineage tracking system to enrich highly pure Th subsets. We began our attempt to produce large numbers of antigen-specific T helper subsets for expression profiling, when Foxp3GFP knockin mice were first made by our laboratory in 2005. We crossed this line with syngeneic TEa TCR transgenic mice in C57BL/6 background, and use FACS to sort optimally stimulated, highly pure GFP(Foxp3)-negative populations for Th1 vs. Th17 expression profile comparison.

ORGANISM(S): Mus musculus

SUBMITTER: Wenda Gao

PROVIDER: E-MTAB-7661 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:In 15 patients with rheumatoid arthritis the baseline expression (t=0) of type I IFN-regulated genes was determined in peripheral blood cells (PAXgene) using cDNA-microarrays and compared to levels one month after (t=1) anti-TNF treatment (infliximab). Therefore, we used 43K cDNA microarrays from the Stanford Functional Genomics Facility (http://microarray.org/sfgf/) printed on aminosilane-coated slides containing ~20.000 unique genes. Only one batch of arrays was used for all experiments. First DNA spots were UV-cross linked to the slide using 150-300 mJoules. Sample preparation and microarray hybridization were performed as described previously (1,2). Data storage and filtering was performed using the Stanford Microarray Database (http://genome-www5.stanford.edu//) as described previously. 1. van der Pouw Kraan TC, Wijbrandts CA, van Baarsen LG, Voskuyl AE, Rustenburg F, Baggen JM et al.: Rheumatoid arthritis subtypes identified by genomic profiling of peripheral blood cells: assignment of a type I interferon signature in a subpopulation of patients. Ann Rheum Dis 2007, 66: 1008-1014. 2. van der Pouw Kraan TC, van Baarsen LG, Rustenburg F, Baltus B, Fero M, Verweij CL: Gene expression profiling in rheumatology. Methods Mol Med 2007, 136: 305-327. Abbreviations: - Bnrs are the different patients analyzed - PAX or Paxgene indicates the total RNA was isolated from peripheral blood obtained in PAXgene tubes - CRS: common reference sample: We made a common reference that consisted of a mixture of mRNAs isolated from 11 different cell lines (Perou CM, Jeffrey SS, van de RM et al. Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. Proc Natl Acad Sci U S A. 1999; 96:9212-9217) supplemented with RNA from rheumatoid synovial tissue, fibroblasts, and activated peripheral blood mononuclear cells (PBMCs). - PMT: photomultiplier tube: the sensitivity/intensity of the scanner can be adjusted to prevent spot saturation. Compound Based Treatment: anti-TNF (infliximab) reference_design

Dataset Information

Compare gene expression profiles of TCR transgenic CD4+ T helper type 1 (Th1) vs. type 17 (Th17) cells optimally stimulated by antigen and differentiated under Th1 or Th17 conditions.

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