Dataset Information

Transcription profiling of mouse naive T cells differentiated under TH1 and TH2 conditions

ABSTRACT: Naive CD4+ CD62L+ CD25- T cells were differentiated under TH1 and TH2 conditions for 7 days, restimulated with anti-CD3 and anti-CD28 for 24h and sorted for IFN-gamma (TH1) and IL-4 (TH2) production using cytokine secretion assays.

INSTRUMENT(S): 418 [Affymetrix]

ORGANISM(S): Mus musculus

SUBMITTER: Barbara Schraml

PROVIDER: E-MEXP-2153 | ArrayExpress | 2009-06-06

REPOSITORIES: ArrayExpress

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Dataset's files

Source:

			Action	DRS
	E-MEXP-2153.README.txt	Txt
	E-MEXP-2153.eSet.r	Other
	E-MEXP-2153.idf.txt	Idf
	E-MEXP-2153.idf.txt_original	Idf
	E-MEXP-2153.processed.1.zip	Processed

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Publications

The AP-1 transcription factor Batf controls T(H)17 differentiation.

Schraml Barbara U BU Hildner Kai K Ise Wataru W Lee Wan-Ling WL Smith Whitney A-E WA Solomon Ben B Sahota Gurmukh G Sim Julia J Mukasa Ryuta R Cemerski Saso S Hatton Robin D RD Stormo Gary D GD Weaver Casey T CT Russell John H JH Murphy Theresa L TL Murphy Kenneth M KM

Nature 20090705 7253

Activator protein 1 (AP-1, also known as JUN) transcription factors are dimers of JUN, FOS, MAF and activating transcription factor (ATF) family proteins characterized by basic region and leucine zipper domains. Many AP-1 proteins contain defined transcriptional activation domains, but BATF and the closely related BATF3 (refs 2, 3) contain only a basic region and leucine zipper, and are considered to be inhibitors of AP-1 activity. Here we show that Batf is required for the differentiation of IL ...[more]

PMID: 19578362

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Project description:In this work we present an analytical strategy to systematically identify early regulators by combining gene regulatory networks (GRN) with GWAS. We hypothesized that early regulators in T-cell associated diseases could be found by defining upstream transcription factors (TFs) in T-cell differentiation. Time series expression and DNA methylation profiling of T-cell differentiation identified several upstream TFs, of which TFs involved in Th1/2 differentiation were most enriched for disease associated SNPs identified by GWAS. Naïve CD4+ T cells were isolated from buffy coat of four healthy donors using a naïve CD4+ T cell isolation kit (Miltenyi, Bergisch-Gladbach, Germany). Naïve CD4+ T cells were stimulated with plate-bound anti-CD3 (500 ng/mL), soluble anti-CD28 (500 ng/mL), in the presence of IL-12 (5 ng/mL), IL-2 (10 ng/mL) and anti–IL-4 (5 µg/mL) for Th1, IL-4 (10 ng/mL), IL-2 (10 ng/mL) and anti-IL-12 (5 µg/mL) and anti–IFN-g (5 µg/mL) for Th2. Cells were cultured for six days in Iscove’s modified Dulbecco medium (IMDM) supplemented with 2 mM L-glutamine (PAA Laboratories, Linz, Austria), 10% heat-inactivated FCS (PAA Laboratories, Linz, Austria), 5 µM β–mercaptoethanol (Sigma-Aldrich, St. Louis, Missouri, USA) and 50 ug/mL gentamicin (Sigma-Aldrich, St. Louis, Missouri, USA). Cells were cultured for 6 days and then re-stimulated with plate-bound anti-CD3 and soluble anti-CD28 in the presence of corresponding polarizing cytokines and antibodies for another 2 days (Zhang et al. 2013). RNA was extracted using a miRneasy Mini Kit (Qiagen). The RNA concentrations were analysed with NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies). For the gene expression microarray analysis, The cRNA was prepared using a Low Input QuickAmp Labeling Kit. For Th1 and Th2 cells the gene expression microarray analysis was performed using SurePrint G3 Human Gene Expression 8x60K microarray kit, according to the manufacture’s instruction (Agilent Technologies).