sRNAomics (sRNA-Seq)
SEEK ID: https://fairdomhub.org/assays/941
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: MicroRNA Profiling
Technology type: Next generation sequencing
Organisms: Solanum tuberosum, Potato virus Y
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Created: 18th Feb 2019 at 18:54
Last updated: 4th Mar 2019 at 16:51
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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).
R code for differential expression analysis of sRNA-Seq.
phasiRNAs and their counts identified in the MOA samples for sRNA-Seq.
phasiRNAs and their RPM normalised counts identified in the MOA samples for sRNA-Seq.
Differential expression of phasiRNAs between various comparison groups (Sheet: comparisons), with log2-fold changes and Benjamini-Hochberg FDR corrected p-values given.
vsiRNAs and their counts identified in the MOA samples for sRNA-Seq.
vsiRNAs and their RPM normalised counts identified in the MOA samples for sRNA-Seq.
Table connecting MOA sample identifiers to GEO identifiers related to sRNAomics dataset.
miRNAs and their counts identified in the MOA samples for sRNA-Seq.
miRNAs and their RPM normalised counts identified in the MOA samples for sRNA-Seq.
Differential expression of miRNAs between various comparison groups (Sheet: comparisons), with log2-fold changes and Benjamini-Hochberg FDR corrected p-values given.
