With frequent fluctuations in global climate, plants often experience co-occurring dry-wet cycles and pathogen infection and this combination adversely affects plant survival. In the past, some studies indicated that morpho-physiological responses of plants to the combined stress are different from the individual stressed plants. However, interaction of drought stressed or drought recovered plants with pathogen has not been widely studied at molecular level. Such studies are important to understand the defense pathways that operate as part of combined stress tolerance mechanism. In this study, Arabidopsis plants were exposed to individual drought stress (soil drying at 40% FC, D), Pseudomonas syringae pv tomato DC3000 (PStDC3000), infection and their combination. Plants recovered from drought stress were also exposed to PStDC3000. Beside we have also infiltrated P. syringae pv tabaci (PSta, non-host pathogen) individually or in combination with drought stress. Using Affymetrix WT gene 1.0 ST array, global transcriptome profiling of plants leaves under individual drought stress and pathogen infection was compared with their combination. Results implicate that plants exposed to combined drought and pathogen stress experience a new state of stress where each combination of stressor and their timing defines the plant responses and thus should be studied explicitly.
Global Transcriptional Analysis Reveals Unique and Shared Responses in Arabidopsis thaliana Exposed to Combined Drought and Pathogen Stress.
Specimen part
View SamplesColumbia (Col) seeds were sown on half-strength Murashige and Skoog (MS) medium, supplemented with 1% sucrose and 0.8% agar and grown vertically in culture room conditions. The 5-d-old homogenous seedlings were washed five times with sterile water and lastly with liquid half strength MS medium without sugar to remove residual exogenous sugar. In order to deplete internal sugars seedlings were grown in sugar free liquid half strength MS medium for 24 h in dark. Thereafter, the seedlings were treated with half-strength MS medium containing 0% G, 0% G + 1 uM BAP, 3% G, and 3% G + 1 uM BAP for 3 h in dark. RNA was extracted and microarray analysis was performed. Please note: G stands for glucose and BAP stands for 6-Benzylaminopurine (cytokinin)
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Age
View SamplesThree bZIP transcription factors (TFs), namely GBF1, HY5, and HYH, form heterodimers with each other and regulate photomorphogenesis in an interdependent manner. GBF1 acts as both a positive and negative regulator of photomorphogenesis, whereas HY5 and HYH mainly act as positive regulators of photomorphogenesis. To study the effect of HY5 and HYH on GBF1-mediated genome-wide expression, transcript profiling was performed in the gbf1 single mutant and gbf1hy5 and gbf1hyh double mutants. Our study revealed that GBF1 mainly acts antagonistic to HY5 and HYH for genome-wide expression.
Genome-wide DNA binding of GBF1 is modulated by its heterodimerizing protein partners, HY5 and HYH.
Age, Specimen part
View SamplesAlthough many regulatory components of light signaling have been functionally characterized, only a few of them have been reported to cross talk with other signaling cascades. In this study, we have analyzed the expression profiles of Arabidopsis genes in wild-type, atmyc2 mutant, cop1-6 mutant, and atmyc2 cop1-6 double mutant seedlings grown under constant dark, constant blue-light, and constant blue-light along with abscisic acid (ABA) to illustrate the interplay of negative regulators, AtMYC2 and COP1, in light and ABA signaling
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No sample metadata fields
View SamplesArabidopsis thaliana seeds after imbibition were inoculated in ½ MS medium supplemented with 0.8% agar and 1% sucrose. Once the plant material was uniformly germinated, the experimental conditions were applied. 5d old light-grown uniformly germinated seedlings were washed seven times with sterile water with last wash given by ½ MS liquid medium without sucrose to remove residual exogenous sugar and the plant material was kept in ½ MS liquid without sucrose in the dark for all subsequent steps. Cultures were shaken at 140 rpm at 22oC for 24 h and then 3 h treatment was given with liquid ½ MS without glucose and liquid ½ MS supplemented with BR (0.1 ?M EBR), glucose (3%), glucose (3%) + BR (0.1 ?M EBR). Seedlings were harvested after 3h and preceded for RNA isolation and Microarray analysis.
Genome wide Analysis of Glucose and Brassinosteroid Signaling Interactions in Arabidopsis thaliana
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Age, Time
View SamplesThis SuperSeries is composed of the SubSeries listed below.
Hypoxia-induced HIF1α targets in melanocytes reveal a molecular profile associated with poor melanoma prognosis.
Specimen part, Cell line
View SamplesThese datasets describe a melanocyte specific, HIF1A-Dependent / Hypoxia-Responsive gene expression signature defined by the regulation of genes critical to metabolism, chromatin and transcriptional regulation, vascularization and cellular invasivness. These genes provide lineage specific targets for refinement of diagnostic markers associated with primary melanoma tumor metastatic potential, and also provides novel molecular targets for therapeutic strategies targeting metastatic disease progression.
Hypoxia-induced HIF1α targets in melanocytes reveal a molecular profile associated with poor melanoma prognosis.
Specimen part, Cell line
View SamplesNucellar embryony is a form of apomixis found in citrus where somatic nucellar cells differentiate into embryos and are included in the seed resulting from the normal sexual process. The nucellar cells giving rise to adventive embryo start proliferating prior to anthesis and fully differentiate obtaining nourishment from sexually derived endosperm. To identify transcripts differentially expressed during nucellar embryo initiation we have taken RNA samplesfrom different developing stages of ovules from polyembryonic (cv. Vaniglia Sanguigno) and monoembryonic (cv. Temple) cultivars. We used microarray for a detailed analysis of global gene expression during nucellar embryony initiation and development. We have further validated the differentially expressed genes using qRT-PCR.
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Specimen part
View SamplesWhole genome transcriptome profiling of bulked RILs with high and low grain number per panicle derived from 2 cultivars at panicle primordia stage
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No sample metadata fields
View SamplesThe aim of this study was to identify candidate genes responsible for grain number per panicle between a pair of rice varieties (Pusa 1266 and Pusa Basmati 1) by combining QTL analysis with expression analysis. Microarray analysis of RNA extracted from the panicle primordia showed 2741 differentially expressed genes. The differentially expressed genes were shortened to 18 on the basis of their occurance in the QTL region (responsible for grain number regulation) detected in RIL population derived from Pusa 1266 and Pusa Basmati 1.
Identification of candidate genes for grain number in rice (Oryza sativa L.).
No sample metadata fields
View Samples