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SEEK ID: https://fairdomhub.org/assays/943
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: Bioinformatics
Technology type: Interactions
Organisms: Solanum tuberosum, Potato virus Y
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Created: 18th Feb 2019 at 19:56
Last updated: 4th Mar 2019 at 17:51
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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)
Novel miRNAs and/or novel MIR loci identified in PVYNTN- and mock-inoculated samples of cv. Désirée and NahG-Désirée potato plants. List of novel/known miRNAs with novel MIR loci. For each miRNA, sequence, length, class (C – conserved or N – novel), miRNA family, the genome locations, strand, the predicted hairpin precursor (pre-miRNA) sequences and the location in genome (MIR loci), their lengths, minimal folding energy index (MFEI; calculated as described by Zhang et al. (2006) as well as gene
...
Investigations: MOA - Multiomics analysis of potato response to...
Studies: MOA2010-05
Assays: sRNAomics (bioinformatics)
PHAS loci identified by genome and transcriptome-wide phasing analysis. List of genome locations for the all identified non-coding PHAS loci or transcript identifiers (IDs) for protein-coding PHAS loci together with the lengths of their producing phasiRNAs. For the protein-coding PHAS loci, transcript full description, protein domains (obtained from PFAM database; Finn et al. 2016), MapMan ontology annotation (from GoMapMan;(Ramšak et al. 2014)) and log2 ratio of gene expression between PVYNTN-infected
...
Investigations: MOA - Multiomics analysis of potato response to...
Studies: MOA2010-05
Assays: sRNAomics (bioinformatics)
Predicted targets of endogenous small RNAs (sRNAs) by in silico approach. For each predicted interaction, miRNAs/phasiRNA ID, the target transcript identifiers, representative gene identifier, short gene name, full descriptions, MapMan ontology annotations (GoMapMan; (Ramšak et al., 2014)) and predicted target regulation (cleavage or translational repression) are shown. Short names for potato genes were inferred from Arabidopsis thaliana orthologs where applicable, else the StNIB_v1 gene identifier
...
Investigations: MOA - Multiomics analysis of potato response to...
Studies: MOA2010-05
Assays: sRNAomics (bioinformatics)
sRNA regulatory network connecting endogenous miRNAs, phasiRNAs and their targets.
Investigations: MOA - Multiomics analysis of potato response to...
Studies: MOA2010-05
Assays: sRNAomics (bioinformatics)
sRNA regulatory network connecting miRNAs, phasiRNAs, PVY-derived siRNAs (vsiRNAs) and their targets.
Investigations: MOA - Multiomics analysis of potato response to...
Studies: MOA2010-05
Assays: sRNAomics (bioinformatics)