Ziva Ramsak

project: _p_stRT Short Name: stRT Title: Solanum tuberosum Reference Transcriptomes Description: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato pISA projects path: ../pISA-Projects Local pISA-tree organisation: National Institute of Biology pISA project creation date: 2019-10-22 pISA project creator: Maja Zagorscak, Ziva Ramsak, Marko Petek Project funding code: This project was supported by the Slovenian Research Agency (grants P4-0165, J4-4165, J4-7636, ...

Our world is changing fast! Key global trends are rapid urbanisation, growing and ageing populations, and increased prosperity. This results in depletion of natural and petrochemical resources and climate change, which affects the quality of the environment and people's lives. Therefore, developing a bio-based economy is key to sustain our planet in the long term. Raw materials will have to be recruited from renewable sources.

Industrial biotechnology is potentially a very powerful technology in ...

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.

Investigation: _I_STRT Short Name: STRT Title: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato Description: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato Phenodata: ./phenodata_20191022.txt pISA Investigation creation date: 2019-10-22 pISA Investigation creator: Maja Zagorscak, Ziva Ramsak, Marko Petek Principal investigator: Kristina Gruden License: MIT Sharing permission: Public Upload to FAIRDOMHub: Yes

RELATED ...

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.

Study: _S_03_stCuSTr Short Name: 03_stCuSTr Title: Solanum tuberosum Cultivar-Specific Transcriptomes Description: Solanum tuberosum Cultivar-Specific Transcriptomes Raw Data: ../_S_01_sequences/, ../_S_02_denovo/ pISA Study creation date: 2019-10-22 pISA Study creator: Maja Zagorscak, Marko Petek, Ziva Ramsak Principal investigator: Kristina Gruden License: MIT Sharing permission: Public Upload to FAIRDOMHub: Yes

RELATED FILES: /reports/README.MD https://fairdomhub.org/documents/346 /_STUDY_METADATA.TXT ...

Hormonomics measurements.

Symptoms obsevation, photosynthetic, pathogen (qPCR), transcriptomics (qPCR, microarrays, Degradome-Seq) and proteomics (MS) measurements.

Description of observed phenotypic variables in the MOA investigation.

Assay: _A_03.2_components Short Name: 03.2_components Assay Class: DRY Assay Type: components Title: Components: tr2aacds headers, cdhit-2d Description: Components: tr2aacds headers, cdhit-2d; post-filtering redefinition of paralogue clusters pISA Assay creation date: 2019-10-22 pISA Assay creator: Ziva Ramsak Phenodata: None Featuredata: Data:

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 the hormone analysis.

R code for differential expression analysis of 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).

Code used for the analysis of microarray data.

Archive containing some phenotyping images (.tar.gz).

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.

miRNA stem-loop RT-qPCR for sRNA-Seq data validation. sRNA expression results obtained by sRNA-seq were validated by stem-loop RT-qPCR. For validation experiments, the same RNA samples as used for sRNA-Seq were analysed.

RT-qPCR assays for sRNA-Seq validation described using the MIQE standard.

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 ...

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 ...

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 ...

sRNA regulatory network connecting endogenous miRNAs, phasiRNAs and their targets.

sRNA regulatory network connecting miRNAs, phasiRNAs, PVY-derived siRNAs (vsiRNAs) and their targets.

Table connecting MOA degradome pool identifiers to GEO identifiers.

Experimentally validated targets of endogenous sRNAs by Degradome-Seq. For each identified interaction, miRNAs/phasiRNA ID, the target transcript identifiers, representative gene identifier, full descriptions, and MapMan ontology annotations (GoMapMan; (Ramšak et al., 2014)) are shown. Short names for potato genes were inferred from Arabidopsis thaliana orthologs where applicable, else the StNIB_v1 gene identifier was set (Ramšak et al., 2014). For each sRNA-target interaction, degradome category ...

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