Transcriptomics (microarrays)
SEEK ID: https://fairdomhub.org/assays/939
Experimental Assay
Projects: MOA - Multiomics analysis of potato response to Potato virus Y (PVY) inf...
Investigation: MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection
Study: MOA2010-05
Assay position:
Assay type: Gene Expression Profiling
Technology type: Custom Array
Organisms: Solanum tuberosum, Potato virus Y
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Created: 18th Feb 2019 at 18:51
Last updated: 4th Mar 2019 at 16:50
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https://orcid.org/0000-0003-0913-2715
National Institute of Biology, Department of Biotechnology and Systems Biology projects
Projects: HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, pISA-tree, MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection, SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture, INDIE - Biotechnological production of sustainable indole, _p_stRT, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato, _p_RNAinVAL, tst, tst2, Playground
Web page: http://www.nib.si/eng/index.php/departments/department-of-biotechnology-and-systems-biology
Time series response of potato cv. Désirée, which is tolerant to PVY infection, was analysed in both inoculated as well as upper non-inoculated leaves. Additionally, transgenic plants deficient in accumulation of salicylic acid (NahG- Désirée) were studied in the same setting.
This investigation is published under the CC BY 4.0 license.
Programme: NIBSys
Public web page: Not specified
Time series response of potato cv. Désirée, which is tolerant to PVY infection, was analysed in both inoculated as well as upper non-inoculated leaves. Additionally, transgenic plants deficient in accumulation of salicylic acid (NahG- Désirée) were studied in the same setting.
All the files available are published under the CC BY 4.0 license.
Symptoms obsevation, photosynthetic, pathogen (qPCR), transcriptomics (qPCR, microarrays, Degradome-Seq) and proteomics (MS) measurements.
Submitter: Ziva Ramsak
Investigation: MOA - Multiomics analysis of potato response to...
Assays: Degradomics, Disease symptoms, Pathogen abundance, Photosynthetic activity, Proteomics, Transcriptomics (microarrays), Transcriptomics (qPCR), sRNAomics (bioinformatics), sRNAomics (qPCR), sRNAomics (sRNA-Seq)
Master table describing all the samples included in MOA Investigation; studies are descrubed using MIAPPE (Minimum Information About a Plant Phenotyping Experiment).
Some additional files required for the R code (phenodata, feature data i.e. the GAL file and Agi4x44PreProcess downloaded package, as it is not maintained on BioConductor anymore).
Code used for the analysis of microarray data.
Table connecting MOA Investigation sample ID's and GEO sample identifiers.
QC filtered and RSN normalised values for all MOA samples with microarray measurements.
Differential expression of genes between various comparison groups (Sheet: comparisons), with log2-fold changes and Benjamini-Hochberg FDR corrected p-values given.
