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Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of Arabidopsis cell culture response to cyclopentenone oxylipins

ABSTRACT: This SuperSeries is composed of the following subset Series: GSE10719: Response of Arabidopsis cell culture to phytoprostane A1; GSE10732: Identification of TGA-regulated genes in response to phytoprostane A1 and OPDA Experiment Overall Design: Refer to individual Series

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Susanne Berger

PROVIDER: E-GEOD-10749 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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General detoxification and stress responses are mediated by oxidized lipids through TGA transcription factors in Arabidopsis.

Mueller Stefan S Hilbert Beate B Dueckershoff Katharina K Roitsch Thomas T Krischke Markus M Mueller Martin J MJ Berger Susanne S

The Plant cell 20080311 3

12-oxo-phytodienoic acid and several phytoprostanes are cyclopentenone oxylipins that are formed via the enzymatic jasmonate pathway and a nonenzymatic, free radical-catalyzed pathway, respectively. Both types of cyclopentenone oxylipins induce the expression of genes related to detoxification, stress responses, and secondary metabolism, a profile clearly distinct from that of the cyclopentanone jasmonic acid. Microarray analyses revealed that 60% of the induction by phytoprostanes and 30% of th ...[more]

PMID: 18334669

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Transcription profiling of Arabidopsis defective in the expression of TGA2, TGA5, and TGA6

Project description:12-oxo-phytodienoic acid (OPDA) and phytoprostane A1 (PPA1) are cyclopentenone oxylipins that are formed via the enzymatic; jasmonate pathway and a nonenzymatic, free radicalâcatalyzed pathway, respectively. Both types of cyclopentenone oxylipins; induce the expression of genes related to detoxification, stress responses, and secondary metabolism, a profile clearly distinct; from that of the cyclopentanone jasmonic acid. To investigate the role of TGA transcriction factors in oxylipin responses, the regulation of gene expression by OPDA and PPA1 defective in; the expression of TGA2, TGA5, and TGA6 was analyzed using; Affymetrix ATH1 chips. Experiment Overall Design: 18 hybs total

2008-06-18 | E-GEOD-10732 | biostudies-arrayexpress

Response of Arabidopsis cell culture to phytoprostane A1

Project description:12-Oxo-phytodienoic acid (OPDA) and several phytoprostanes are structurally related cyclopentenone oxylipins that can be formed via the enzymatic jasmonate pathway and a non-enzymatic, free radical-catalyzed pathway, respectively. To elucidate the biological activities of phytoprostanes in comparison to OPDA as well as the metabolism we performed genome-wide expression analysis. Experiment Overall Design: In order to get a comprehensive view of the biological activity of non-enzymatically formed reactive oxylipins the regulation of gene expression in Arabidopsis thaliana was analyzed using the ATH1 chip representing 22500 genes. A mixotrophic cell culture of Arabidopsis was treated with 75 ÂµM phytoprostane A1 or with 0.5% methanol in water (Control) and harvested after 4 h. Three independent replicates of each treatment were analyzed and the fold change of normalized signals from PPA1-treated cell culture versus control cell culture was calculated.

2008-06-18 | E-GEOD-10719 | biostudies-arrayexpress

Arabidopsis thaliana

Project description:Identification of TGA-regulated genes in response to phytoprostane A1 and OPDA

| PRJNA108863 | ENA

Identification of TGA-regulated genes in response to phytoprostane A1 and OPDA

Project description:12-oxo-phytodienoic acid (OPDA) and phytoprostane A1 (PPA1) are cyclopentenone oxylipins that are formed via the enzymatic jasmonate pathway and a nonenzymatic, free radical–catalyzed pathway, respectively. Both types of cyclopentenone oxylipins induce the expression of genes related to detoxification, stress responses, and secondary metabolism, a profile clearly distinct from that of the cyclopentanone jasmonic acid. To investigate the role of TGA transcriction factors in oxylipin responses, the regulation of gene expression by OPDA and PPA1 defective in the expression of TGA2, TGA5, and TGA6 was analyzed using Affymetrix ATH1 chips. Keywords: Arabidopsis tga2-5-6 mutant, Oxylipin treatment, ATH1 Chip

2008-06-02 | GSE10732 | GEO

Response of Arabidopsis cell culture to phytoprostane A1

2008-06-02 | GSE10719 | GEO

Transcription profiling of zebrafish development

Project description:We are performing microarray experiments for expression profiling of zebrafish embryogenesis, both as a baseline for future analysis of mutant and other conditions and to validate our microarray technology. For our purpose we used the Affymetrix zebrafish array which contains approximately 15,000 genes. This represents about 50 % of the estimated number of zebrafish genes. Total RNA was collected from embryos at 16 different stages (zygote, shield stage, 75 % epiboly, 90 % epiboly, bud stage, 5-somite stage, 14-somite stage, prim-5 stage, 32 hpf and long-pec stage, 4d post fertilization (dpf), 5 dpf, 14 dpf, 30 dpf, 90 dpf, adult). Microarray analysis was performed with these stages in single colour experiments. After normalization, differential expressed genes were selected and further analyzed with GeneSpring software. In order to validate the microarray data and to assign biological functions we chose a few genes to do semi-quantitative real-time PCR. Many of the differentially expressed genes are unknown and could be candidates for regulatory genes identified in mutagenesis experiments. We identified several genes known to be involved in zebrafish organogenesis as well as novel genes with unique temporal expression patterns.

2005-08-18 | E-TABM-33 | biostudies-arrayexpress

Transcription profiling of zebrafish cls/sox10 mutants at 4dpf compared to their wild type siblings at 4 day identifies lndc1 as a novel factor in Schwann cell development

Project description:Transcription profile of cls/sox10 mutants at 4dpf compared to their wild type siblings at 4 days post fertilization. Transcription profile of hps/erbb3b mutants compared to a wild type control at 4 days post fertilization.

2009-12-15 | E-MEXP-2215 | biostudies-arrayexpress

Transcription profiling of mouse bladder urothelium

Project description:Host responses to intracellular UPEC communities; We used laser capture microdissection and microarrays to identify urothelial transcripts differentially expressed in response to proximity to intracellular UPEC. Experiment Overall Design: Transcription within four distinct populations of urothelial cells was profiled in biological duplicate: (i) uninfected, (ii) mock-infected (sterile 1x PBS), (iii) IBC-distal (cells residing >10 cell diameters from IBCs in the section plane), and (iv) IBC-proximal (cells residing <10 cell diameters from IBCs in the section plane).

2008-06-14 | E-GEOD-6419 | biostudies-arrayexpress

Transcription profiling of mouse rhombomere 4 at E10.5 from knockins of Hoxb1 gene expressing Hox-A1 protein

Project description:This study analyzed mRNA profiles in rhombomere 4 of E10.5 mouse knock-in embryos expressing either normal endogenous Hox-B1 protein or the paralogous Hox-A1 protein from the Hoxb1 locus. The Hox-A1 protein was found to be detectably less efficacious than Hox-B1 in promoting neurogenesis in the basal plate of rhombomere 4 and its transcriptional profile shared several similarities with the Hoxb1 mutant. Experiment Overall Design: GFP-positive cells were FACS-sorted from dissected hindbrains of entire litters of E10.5 mouse embryos expressing either normal endogenous Hox-B1 protein or the paralogous Hox-A1 protein from the Hoxb1 locus, either one tagged with IRES-tauGFP. Three independent biological replicates of each genotype were analyzed. Total RNA was isolated, amplified and hybridized to Affymetrix Mouse Genome 430 2.0 Arrays.

2008-06-13 | E-GEOD-5124 | biostudies-arrayexpress

Transcription profiling of Populus stress response: nitrogen limitation, leaf wounding, and methyl jasmonate feeding of cell culture

Project description:This SuperSeries is composed of the following subset Series:; GSE16773: Gene expression response of Populus tremuloides cell suspension cultures to methyl jasmonate feeding; GSE16783: Wound-induced gene expression changes in Populus: 1 week; GSE16785: Wound-induced gene expression changes in Populus: 90 hours; GSE14893: Comparative transcriptomics analysis of Populus leaves under nitrogen limitation: clone 3200; GSE14515: Comparative transcriptomics analysis of Populus leaves under nitrogen limitation: clone 1979 Experiment Overall Design: Refer to individual Series

2009-12-14 | E-GEOD-16786 | biostudies-arrayexpress

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