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Transcriptional profiling of apoptosis-deficient Drosophila mutants.

ABSTRACT: Apoptosis is a fundamental way to remove damaged or unwanted cells during both developmental and post-developmental stages. Apoptosis deficiency leads to various diseases including cancer. To know the physiological changes in apoptosis-deficient mutants, we conducted non-biased transcriptomic analysis of Drosophila dark(cd4) mutants. As recently reported, combined with metabolome and genetic analysis, we identified systemic immune response, energy wasting, as well as alteration in S-adenosyl-methionine metabolism in response to necrotic cells [1]. Here, we describe in detail how we obtained validated microarray dataset deposited in Gene Expression Omnibus (GSE47853). Our data provide a resource for searching transcriptional alterations in Drosophila apoptosis-deficient mutants.

SUBMITTER: Obata F

PROVIDER: S-EPMC4535892 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature

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Transcriptional profiling of apoptosis-deficient Drosophila mutants.

Obata Fumiaki F Tomioka Katsura K Miura Masayuki M

Genomics data 20140810

Apoptosis is a fundamental way to remove damaged or unwanted cells during both developmental and post-developmental stages. Apoptosis deficiency leads to various diseases including cancer. To know the physiological changes in apoptosis-deficient mutants, we conducted non-biased transcriptomic analysis of Drosophila dark(cd4) mutants. As recently reported, combined with metabolome and genetic analysis, we identified systemic immune response, energy wasting, as well as alteration in S-adenosyl-met ...[more]

PMID: 26484104

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Project description:BACKGROUND: Arabidopsis ovules comprise four morphologically distinct parts: the nucellus, which contains the embryo sac, two integuments that become the seed coat, and the funiculus that anchors the ovule within the carpel. Analysis of developmental mutants has shown that ovule morphogenesis relies on tightly regulated genetic interactions that can serve as a model for developmental regulation. Redundancy, pleiotropic effects and subtle phenotypes may preclude identification of mutants affecting some processes in screens for phenotypic changes. Expression-based gene discovery can be used access such obscured genes. RESULTS: Affymetrix microarrays were used for expression-based gene discovery to identify sets of genes expressed in either or both integuments. The genes were identified by comparison of pistil mRNA from wild type with mRNA from two mutants; inner no outer (ino, which lacks the outer integument), and aintegumenta (ant, which lacks both integuments). Pools of pistils representing early and late stages of ovule development were evaluated and data from the three genotypes were used to designate genes that were predominantly expressed in the integuments using pair-wise and cluster analyses. Approximately two hundred genes were found to have a high probability of preferential expression in these structures, and the predictive nature of the expression classes was confirmed with reverse transcriptase polymerase chain reaction and in situ hybridization. CONCLUSION: The results showed that it was possible to use a mutant, ant, with broad effects on plant phenotype to identify genes expressed specifically in ovules, when coupled with predictions from known gene expression patterns, or in combination with a more specific mutant, ino. Robust microarray averaging (RMA) analysis of array data provided the most reliable comparisons, especially for weakly expressed genes. The studies yielded an over-abundance of transcriptional regulators in the identified genes, and these form a set of candidate genes for evaluation of roles in ovule development using reverse genetics.

Dataset Information

Transcriptional profiling of apoptosis-deficient Drosophila mutants.

Publications

Transcriptional profiling of apoptosis-deficient Drosophila mutants.

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