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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 type: Gene Expression Profiling
Technology type: Custom Array
Organisms: Solanum tuberosum, Potato virus Y
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Created: 18th Feb 2019 at 19:51
Last updated: 4th Mar 2019 at 17:50
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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
Organisms: Potato virus Y, Solanum tuberosum
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.
Snapshots: Snapshot 1, Snapshot 2, Snapshot 3, Snapshot 4, Snapshot 5
Symptoms obsevation, photosynthetic, pathogen (qPCR), transcriptomics (qPCR, microarrays, Degradome-Seq) and proteomics (MS) measurements.
Person responsible: Ziva Ramsak
Snapshots: No snapshots
Master table describing all the samples included in MOA Investigation; studies are descrubed using MIAPPE (Minimum Information About a Plant Phenotyping Experiment).
Investigations: MOA - Multiomics analysis of potato response to...
Studies: MOA2010-05, MOA2013-12
Assays: Degradomics, Disease symptoms, Hormone concentrations, Pathogen abundance, Photosynthetic activity, Proteomics, Transcriptomics (microarrays), Transcriptomics (qPCR), sRNAomics (bioinformatics), sRNAomics (qPCR), sRNAomics (sRNA-Seq)
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).
Investigations: MOA - Multiomics analysis of potato response to...
Studies: MOA2010-05
Assays: Transcriptomics (microarrays)
Code used for the analysis of microarray data.
Investigations: MOA - Multiomics analysis of potato response to...
Studies: MOA2010-05
Assays: Transcriptomics (microarrays)
Table connecting MOA Investigation sample ID's and GEO sample identifiers.
Investigations: MOA - Multiomics analysis of potato response to...
Studies: MOA2010-05
Assays: Transcriptomics (microarrays)
QC filtered and RSN normalised values for all MOA samples with microarray measurements.
Investigations: MOA - Multiomics analysis of potato response to...
Studies: MOA2010-05
Assays: Transcriptomics (microarrays)
Differential expression of genes between various comparison groups (Sheet: comparisons), with log2-fold changes and Benjamini-Hochberg FDR corrected p-values given.
Investigations: MOA - Multiomics analysis of potato response to...
Studies: MOA2010-05
Assays: Transcriptomics (microarrays)