Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of greenhouse grown wheat treated with three antifungal compounds (BTH, Azoxystrobin or Fenpropimorph)

ABSTRACT: Effect of three antifungal compounds (BTH, Azoxystrobin or Fenpropimorph) on wheat gene expression.

ORGANISM(S): Triticum aestivum

SUBMITTER: Jürg Zarn

PROVIDER: E-MEXP-314 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

HOXA genes are included in genetic and biologic networks defining human acute T-cell leukemia (T-ALL).

Soulier Jean J Clappier Emmanuelle E Cayuela Jean-Michel JM Regnault Armelle A García-Peydró Marina M Dombret Hervé H Baruchel André A Toribio Maria-Luisa ML Sigaux François F

Blood 20050317 1

Using a combination of molecular cytogenetic and large-scale expression analysis in human T-cell acute lymphoblastic leukemias (T-ALLs), we identified and characterized a new recurrent chromosomal translocation, targeting the major homeobox gene cluster HOXA and the TCRB locus. Real-time quantitative polymerase chain reaction (RQ-PCR) analysis showed that the expression of the whole HOXA gene cluster was dramatically dysregulated in the HOXA-rearranged cases, and also in MLL and CALM-AF10-relate ...[more]

PMID: 15774621

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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 of greenhouse grown wheat treated with three antifungal compounds (BTH, Azoxystrobin or Fenpropimorph)

Publications

HOXA genes are included in genetic and biologic networks defining human acute T-cell leukemia (T-ALL).

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