Transcripomic analysis of leaf gene expression in S and N-deficient winter wheat during grain development. Tissue was harvested at anthesis and 7, 14 and 21 days post anthesis from experimental field plots.
Co-ordinated expression of amino acid metabolism in response to N and S deficiency during wheat grain filling.
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Specimen part, Disease, Disease stage, Subject, Time
View SamplesMutations mapping to the RNA-binding interface of EXOSC3 have been linked to the rare neurological disorder known as Pontocerebellar Hypoplasia type1B (PCH1B). EXOSC3 is part of three putative RNA-binding structural cap proteinsthat guideRNA intothe RNA exosome, thecellular machinery that2degrades RNA. Here, using RNAcompete, we identifieda G-rich RNA motifthat requirestheK homology and ribosomal protein S1domains of EXOSC3. Interestingly, several PCH1B-causing mutations in EXOSC3do not engage this RNA motif. To test the hypothesis thatmodificationof the RNA-protein interface in EXOSC3 mutants may be phenocopied by small molecules, we performedan in silicoscreen of 50,000 small molecules and used enzyme-linked immunosorbant assays(ELISAs)to assess the ability ofthe molecules to inhibit RNA-bindingbyEXOSC3. We identified asmall molecule, EXOSC3-RNA disrupting (ERD) compound 3 (ERD03), which: (i) bound specifically to EXOSC3in saturation transfer difference nuclear magnetic resonance (STD NMR); (ii)disruptedthe EXOSC3-RNAinteraction in a concentration-dependent manner; (iii) induced an abnormal curved spine PCH1B-like phenotype in zebrafish embryos.This compound induced a comparable modification of RNA expression levels coupled with an atrophy of the cerebellum in the zebrafish. To our knowledge, this is the first example of a small molecule obtained by rational design thatmodelsthe abnormal developmental effectsof a neurodegenerative diseasein a whole organism.
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Sex, Age, Specimen part, Disease, Treatment
View SamplesWild type and transgenic msi1-tap1 plants were grown and gene expression was compared at two time points at the age of 8 days.
Regulation of flowering time by Arabidopsis MSI1.
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Age, Time
View SamplesTime-course analysis of shade responsive genes in Col and 12 mutants.
No associated publication
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Specimen part, Treatment
View SamplesTime-course data of shade avoidance in NAM parents
No associated publication
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Specimen part, Treatment
View SamplesDevelopmental gradient of expanding maize leaf
No associated publication
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Age, Specimen part
View SamplesA model system of Potyvirus turnip mosaic virus and Arabidopsis was used in this experiment. GFP-tagged virus supplied a visualized marker for us to localize the viral infection foci and its expansion on leaf under UV light. Initially, we dissect an individual infection focus and its adjacent region into four parts and define those four parts as zone 0, 1, 2, and 3, which represented different viral infection stages respectively. Corresponding fours parts were also dissected from control plant treated with turnip leaf sap only. This process was replicated three times totally.
Spatial analysis of arabidopsis thaliana gene expression in response to Turnip mosaic virus infection.
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Age, Specimen part
View SamplesPro35SLBD16:GR or Pro35SLBD18:GR transgenic seedlings that overexpress LBD16 or LBD18 fused to glucocorticoidsteroid hormone binding domain(GR) under CaMV35S promoter were grown for 12 days under long-day conditions (16h light/ 8h dark).
LBD18 acts as a transcriptional activator that directly binds to the EXPANSIN14 promoter in promoting lateral root emergence of Arabidopsis.
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Specimen part, Compound, Time
View SamplesSoybean transcript fluctuations were observed in response to Rhizoctonia solani AG-1 IA causing Rhizoctonia foliar blight. The overall goal was to observe the general transcriptome fluctuations using RNAseq Illumina HiSeq analysis.
No associated publication
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Specimen part, Disease
View SamplesIn order to study the gene expression of pollen tubes as they grow in silk after pollination, we pollinated maize W22 silks with maize B73 pollen. The recent (2016) advent of the W22 genome assembly and annotation allows us to single out RNA-seq reads originating from the pollen tubes. B73 pollen, W22 silk and B73 seedling controls were sequenced as well.
No associated publication
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Specimen part
View Samples