Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling time course of field grown wheat plants treated with three antifungal compounds: BTH, Azoxystrobin and Fenpropimorph

ABSTRACT: Wheat plants, grown in the field, were treated with three antifungal compounds: BTH, Azoxystrobin and Fenpropimorph. Gene expression changes were assessed 24hrs, 1 and 2 weeks after treatment.

ORGANISM(S): Triticum aestivum

SUBMITTER: Beat Keller

PROVIDER: E-MEXP-315 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Specific patterns of changes in wheat gene expression after treatment with three antifungal compounds.

Pasquer Frédérique F Isidore Edwige E Zarn Jürg J Keller Beat B

Plant molecular biology 20050301 5

The two fungicides azoxystrobin and fenpropimorph are used against powdery mildew and rust diseases in wheat (Triticum aestivumL). Azoxystrobin, a strobilurin, inhibits fungal mitochondrial respiration and fenpropimorph, a morpholin, represses biosynthesis of ergosterol, the major sterol of fungal membranes. Although the fungitoxic activity of these compounds is well understood, their effects on plant metabolism remain unclear. In contrast to the fungicides which directly affect pathogen metabol ...[more]

PMID: 15988564

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Project description:Profiling miRNA levels in cells with miRNA-microarrays is becoming a widely used technique. Although normalization methods for mRNA gene expression arrays are well established, miRNA array normalization has so far not been investigated in detail. In this study we investigate the impact of normalization on data generated with the Agilent miRNA array platform. Here, we developed a method to select non-changing miRNAs (“invariants”) and used them to compute linear regression normalization coefficients or Variance Stabilizing Normalization (VSN) parameters. We compared the invariant normalizations to normalization by, scaling, quantile and VSN with default parameters as well as to no normalization using samples with strong differential expression of miRNAs (heart-brain comparison) and samples where only few miRNAs are affected (p53 overexpression in SCC13 cells versus GFP vector control transfected cells). All normalization methods performed better than no normalization. Normalizations procedures based on the set of invariants and quantile were the most robust over all experimental conditions tested. Our method of invariant selection and normalization is not limited to Agilent miRNA arrays and can be applied to other datasets from one color miRNA microarray platforms, focused gene expression arrays and gene expression analysis using quantitative PCR. Keywords: miRNA profiling To assay technical reproducibility, 3 technical replicates from brain and heart RNA (Stratagene) were hybridized on Agilent human miRNA microarrays. To determine sensitivity and specificity, heart and brain RNA were mixed in the following ratios: 50% heart 50% brain, 25% heart 75% brain and 5% heart 95% brain. Each of the dilutions was hybridized in a technical duplicate on Agilent human miRNA arrays. To assay the effect of p53 expression on miRNA levels in the human SCC13 cell line, RNA from 3 biological replicates of p53-expressing or control cells were hybridized in technical duplicates on the microarrays, resulting in a total of 12 hybridizations.

Dataset Information

Transcription profiling time course of field grown wheat plants treated with three antifungal compounds: BTH, Azoxystrobin and Fenpropimorph

Publications

Specific patterns of changes in wheat gene expression after treatment with three antifungal compounds.

Similar Datasets

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