Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of human primary T cell culture and T cell response to oxidative stress

ABSTRACT: Little is known about the global transcriptional program underlying T-cell activation and T-cell response to oxidative stress. Using DNA microarrays and Q-RT-PCR, we examined the transcriptional profile of human T-cell activation and T-cell response to H2O2 stress. The goal of this study was to identify genes involved in the various facets of human T-cell activation and T-cell response to H2O2 stress. Experiment Overall Design: T cells isolated from peripheral blood were cultured with CD3, CD28, and IL-2 to induce T-cell activaiton. Samples were splited into two parts before the cutlure started, one treated with 25 uM H2O2 for 10 minutes, the other intact. At each timepoint, cells were harvested and frozen for RNA isolation. Three biological replicate experiments were analyzed and approximately one-half of the samples from each experiment were technically replicated. Hybridizations were performed in a reference design with all samples labeled with Cy3 and a reference thymus total RNA labeled with Cy5.

ORGANISM(S): Homo sapiens

SUBMITTER: Eleftherios Papoutsakis

PROVIDER: E-GEOD-6607 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Regulation of gene expression by reactive oxygen species (ROS) is an important component of abiotic stress signal transduction mechanisms. Previous genome-wide analysis of chilling-induced changes in gene expression suggested a potential role of H2O2 and other ROS as key signals in the induction of early response genes in japonica rice (cv. Nipponbare). Candidate regulators including bZIP-, Myb- or WRKY-types of transcription factors that were responsive to both chilling (10oC) and exogenous H2O2, and their probable target clusters (as1/ocs/TGA1-like, MybR-like element containing genes) were inferred by integrative analysis of qPCR expression profiles and ab initio promoter motif data. In an effort to define the composition and hierarchical organization of the ROS-mediated chilling response regulatory networks, we examined the effect of exogenous H2O2 (6 hours in 4mM H2O2 at 28oC and then 6 hours of recovery in water at 28oC) on the transcriptome of Nipponbare in a genome-wide scale and compared them with the chilling stress transcriptome. Results of this study were consistent with our earlier model that a ROSbZIP-as1/ocs/TGA1 regulatory module is a direct consequence of chilling-induced elevation of intracellular ROS during the initial 24 hours. Keywords: time course (response to exogenous H2O2) This experiment describes the analysis of the temporal changes in gene expression in response to exogenous H2O2 in Nipponbare rice. A total of 5 treatment regimes were examined (1, 3, and 6 hours at 4 mM H2O2 and then 3 and 6 hours of recovery in water after 6 hours of exposure to H2O2). The microarray platform used in this study was the 45K oligonucleotide microarray (www.ricearray.org) which comes in pairs of slides A and B (each containing about 50% of the total number of features). The data described in this series include all hybridizations with slide A and with slide B. All experiments were performed with two independent biological replicates (R1 and R2) for each time point.

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Transcription profiling of human primary T cell culture and T cell response to oxidative stress

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