Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of Arabidopsis KZ10/Mrk-0 hybrids and their parents grown at 16C in long day conditions

ABSTRACT: KZ10/Mrk-0 F1 hybrids and their parents were grown at 23 degreeC long days for 12 days then shifted to 16 degreeC and harvested after 2 days. Whole rosettes were harvested, and each sample is a pool of ten plants.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Kirsten Bomblies

PROVIDER: E-ATMX-25 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Autoimmune response as a mechanism for a Dobzhansky-Muller-type incompatibility syndrome in plants.

Bomblies Kirsten K Lempe Janne J Epple Petra P Warthmann Norman N Lanz Christa C Dangl Jeffery L JL Weigel Detlef D

PLoS biology 20070901 9

Epistatic interactions between genes are a major factor in evolution. Hybrid necrosis is an example of a deleterious phenotype caused by epistatic interactions that is observed in many intra- and interspecific plant hybrids. A large number of hybrid necrosis cases share phenotypic similarities, suggesting a common underlying mechanism across a wide range of plant species. Here, we report that approximately 2% of intraspecific crosses in Arabidopsis thaliana yield F1 progeny that express necrosis ...[more]

PMID: 17803357

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Project description:Songbirds provide rich natural models for studying the relationships of brain anatomy, behavioral function, environmental signals and gene expression. Under the Songbird Neurogenomics Initiative, investigators from more than a dozen laboratories collected brain samples from six species of songbird under a range of experimental conditions, and 488 of these samples were analyzed systematically for gene expression by microarray. ANOVA was used to test 32 planned contrasts in the data, revealing the relative impact of different factors. The brain region from which tissue was taken had the greatest influence on gene expression profile, affecting the majority of signals measured by the 18,848 non-redundant cDNAs spotted on the microarray. Social and environmental manipulations had highly variable impact, ranging from nil in some cases to robust in others. Several specific genes were identified as points of interest in the evolution of mechanisms by which environmental signals influence behavior. The data were also analyzed using Weighted Gene Co-expression Network Analysis (WGCNA) followed by Gene Ontology (GO) analysis. This revealed modules of co-regulated genes that are also enriched for specific functional annotations such as M-bM-^@M-^\ribosomeM-bM-^@M-^] (expressed more highly in juvenile brain) and M-bM-^@M-^\dopamine metabolic processM-bM-^@M-^] (expressed more highly in striatal song control nucleus Area X). These results underscore the complexity of influences on neural gene expression and provide a resource for studying how these influences are integrated during natural experience. RNA samples were collected from six different songbird species (phylogeny in SI Appendix, Figure S1) and representing 80 different M-bM-^@M-^\treatmentsM-bM-^@M-^], i.e., combinations of species, brain region, sex, age, and behavioral state. The tissue samples were organized around 15 standalone experiments (Table 1 and SI Appendix, Table S1), contributed by investigators in a dozen different laboratories but analyzed under uniform conditions in a single laboratory as originally planned under the Songbird Neurogenomics Initiative. Each sample was hybridized to a zebra finch cDNA array along with a universal reference (a pool of zebra finch telencephalic RNA). e08: Comparing Area X, HVC, POA and RA from adult male European starlings (Sturnus vulgaris) that were gonadally-intact and photostimulated (7 and 21 days on long days, 16:8 light: dark), castrated and photostimulated (7 days on long days), and photorefractory (56 days on long days), with short-day control (56 days on short days, 11:13 light:dark), 6 biological replicates per group. All samples were hybridized against the SoNG universal RNA reference pool.

Dataset Information

Transcription profiling of Arabidopsis KZ10/Mrk-0 hybrids and their parents grown at 16C in long day conditions

Publications

Autoimmune response as a mechanism for a Dobzhansky-Muller-type incompatibility syndrome in plants.

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