MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection

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.

DOI: 10.15490/fairdomhub.1.investigation.275.5

Created at: 30th Jul 2019 at 10:53

Contents

MOA2010-05

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

Disease symptoms

Description of observed phenotypic variables in the MOA investigation.

MOA_Multiomics-Analysis_Phenodata-n-MIAPPE

Master table describing all the samples included in MOA Investigation; studies are descrubed using MIAPPE (Minimum Information About a Plant Phenotyping Experiment).

  • MOA_Multiomics-Analysis_Phenodata-n-MIAPPE.xlsx

MOA2010-05_1A_disease-symptoms

File describing the phenotypic observations taken on potato plants, namely spot necroses, vein necroses, chlorotic spots, yellowing and mechanicam damage.

  • MOA2010-05_1A_disease-symptoms.xlsx

MOA2010-05_1A_disease-symptoms-images

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

  • MOA2010-05_1A_disease-symptoms-images.tar.gz

Photosynthetic activity

No description specified

MOA_Multiomics-Analysis_Phenodata-n-MIAPPE

Master table describing all the samples included in MOA Investigation; studies are descrubed using MIAPPE (Minimum Information About a Plant Phenotyping Experiment).

  • MOA_Multiomics-Analysis_Phenodata-n-MIAPPE.xlsx

MOA2010-05_1B_photosynthetic-activity

Measurements of photosynthetic activity, namely net photosynthesis (Pn), stomatal conductance (Cond), actual photochemical efficiency (Fv’/Fm’), potential photochemical activity (Fv/Fm), chlorophyll content (SPAD) and electron transport rate (ETR).

  • MOA2010-05_1B_photosynthetic-activity.xlsx

MOA2010-05_1B_photosynthetic-activity_LM

Statistical analysis of measurements of photosynthetic parameters.

  • MOA2010-05_1B_photosynthetic-activity_LM.xlsx

Pathogen abundance

No description specified

MOA_Multiomics-Analysis_Phenodata-n-MIAPPE

Master table describing all the samples included in MOA Investigation; studies are descrubed using MIAPPE (Minimum Information About a Plant Phenotyping Experiment).

  • MOA_Multiomics-Analysis_Phenodata-n-MIAPPE.xlsx

MOA2010-05_1C_pathogen-abundance_qPCR

qPCR measured values of Potato virus Y (PVY).

  • MOA2010-05_1C_pathogen-abundance_qPCR.xlsx

Transcriptomics (microarrays)

No description specified

MOA_Multiomics-Analysis_Phenodata-n-MIAPPE

Master table describing all the samples included in MOA Investigation; studies are descrubed using MIAPPE (Minimum Information About a Plant Phenotyping Experiment).

  • MOA_Multiomics-Analysis_Phenodata-n-MIAPPE.xlsx

MOA2010-05_2_transcriptomics_microarrays_GEO

Table connecting MOA Investigation sample ID's and GEO sample identifiers.

  • MOA2010-05_2_transcriptomics_microarrays_GEO.xlsx

MOA2010-05_2_transcriptomics_microarrays_normalised

QC filtered and RSN normalised values for all MOA samples with microarray measurements.

  • MOA2010-05_2_transcriptomics_microarrays_normalised.xlsx

MOA2010-05_2_transcriptomics_microarrays_logFC

Differential expression of genes between various comparison groups (Sheet: comparisons), with log2-fold changes and Benjamini-Hochberg FDR corrected p-values given.

  • MOA2010-05_2_transcriptomics_microarrays_logFC.xlsx

MOA2010-05_2_transcriptomics_microarrays_R-code

Code used for the analysis of microarray data.

  • MOA2010-05_2_transcriptomics_microarrays_R-code.r

MOA2010-05_2_transcriptomics_microarrays_R-code-inputs

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).

  • MOA2010-05_2_transcriptomics_microarrays_R-code-inputs.tar.gz

Transcriptomics (qPCR)

No description specified

MOA_Multiomics-Analysis_Phenodata-n-MIAPPE

Master table describing all the samples included in MOA Investigation; studies are descrubed using MIAPPE (Minimum Information About a Plant Phenotyping Experiment).

  • MOA_Multiomics-Analysis_Phenodata-n-MIAPPE.xlsx

MOA2010-05_2_transcriptomics_qPCR

Validation of microarray results by RT-qPCR. RT-qPCR measurements for eight genes: biologically relevant for photosynthesis chlorophyll a-b binding protein (CAB, CAB_NEW) and RuBisCO activase (RA); for defense response three classes of β-1,3-glucanases (Glu-I, Glu-II, Glu-III) and pathogenesis-related protein1b (PR-1b); and for sugar metabolism granule bound starch synthase I (GBSSI) and cell wall invertase (INV).

  • MOA2010-05_2_transcriptomics_qPCR.xlsx

MOA2010-05_2_transcriptomics_qPCR_MIQE

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

  • MOA2010-05_2_transcriptomics_qPCR_MIQE.xlsx

sRNAomics (sRNA-Seq)

No description specified

MOA_Multiomics-Analysis_Phenodata-n-MIAPPE

Master table describing all the samples included in MOA Investigation; studies are descrubed using MIAPPE (Minimum Information About a Plant Phenotyping Experiment).

  • MOA_Multiomics-Analysis_Phenodata-n-MIAPPE.xlsx

MOA2010-05_3_sRNAomics_sRNA-Seq_GEO

Table connecting MOA sample identifiers to GEO identifiers related to sRNAomics dataset.

  • MOA2010-05_3_sRNAomics_sRNA-Seq_GEO.xlsx

MOA2010-05_3_sRNAomics_sRNA-Seq_miRNAs_counts

miRNAs and their counts identified in the MOA samples for sRNA-Seq.

  • MOA2010-05_3_sRNAomics_sRNA-Seq_miRNAs_counts.xlsx

MOA2010-05_3_sRNAomics_sRNA-Seq_miRNAs_counts_RPM

miRNAs and their RPM normalised counts identified in the MOA samples for sRNA-Seq.

  • MOA2010-05_3_sRNAomics_sRNA-Seq_miRNAs_counts_RPM.xlsx

MOA2010-05_3_sRNAomics_sRNA-Seq_miRNAs_logFC

Differential expression of miRNAs between various comparison groups (Sheet: comparisons), with log2-fold changes and Benjamini-Hochberg FDR corrected p-values given.

  • MOA2010-05_3_sRNAomics_sRNA-Seq_miRNAs_logFC.xlsx

MOA2010-05_3_sRNAomics_sRNA-Seq_phasiRNAs_counts

phasiRNAs and their counts identified in the MOA samples for sRNA-Seq.

  • MOA2010-05_3_sRNAomics_sRNA-Seq_phasiRNAs_counts.xlsx

MOA2010-05_3_sRNAomics_sRNA-Seq_phasiRNAs_counts_RPM

phasiRNAs and their RPM normalised counts identified in the MOA samples for sRNA-Seq.

  • MOA2010-05_3_sRNAomics_sRNA-Seq_phasiRNAs_counts_RPM.xlsx

MOA2010-05_3_sRNAomics_sRNA-Seq_phasiRNAs_logFC

Differential expression of phasiRNAs between various comparison groups (Sheet: comparisons), with log2-fold changes and Benjamini-Hochberg FDR corrected p-values given.

  • MOA2010-05_3_sRNAomics_sRNA-Seq_phasiRNAs_logFC.xlsx

MOA2010-05_3_sRNAomics_sRNA-Seq_vsiRNAs_counts

vsiRNAs and their counts identified in the MOA samples for sRNA-Seq.

  • MOA2010-05_3_sRNAomics_sRNA-Seq_vsiRNAs_counts.xlsx

MOA2010-05_3_sRNAomics_sRNA-Seq_vsiRNAs_counts_RPM

vsiRNAs and their RPM normalised counts identified in the MOA samples for sRNA-Seq.

  • MOA2010-05_3_sRNAomics_sRNA-Seq_vsiRNAs_counts_RPM.xlsx

MOA2010-05_3_sRNAomics_sRNA-Seq_R-code

R code for differential expression analysis of sRNA-Seq.

  • MOA2010-05_3_sRNAomics_sRNA-Seq_R-code.r

sRNAomics (qPCR)

No description specified

MOA_Multiomics-Analysis_Phenodata-n-MIAPPE

Master table describing all the samples included in MOA Investigation; studies are descrubed using MIAPPE (Minimum Information About a Plant Phenotyping Experiment).

  • MOA_Multiomics-Analysis_Phenodata-n-MIAPPE.xlsx

MOA2010-05_3_sRNAomics_qPCR

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.

  • MOA2010-05_3_sRNAomics_qPCR.xlsx

MOA2010-05_3_sRNAomics_qPCR_MIQE

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

  • MOA2010-05_3_sRNAomics_qPCR_MIQE.xlsx

sRNAomics (bioinformatics)

No description specified

MOA_Multiomics-Analysis_Phenodata-n-MIAPPE

Master table describing all the samples included in MOA Investigation; studies are descrubed using MIAPPE (Minimum Information About a Plant Phenotyping Experiment).

  • MOA_Multiomics-Analysis_Phenodata-n-MIAPPE.xlsx

MOA2010-05_3C_sRNAomics_bioinformatics_miRNA-novel

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
...

  • MOA2010-05_3C_sRNAomics_bioinformatics_miRNA-novel.xlsx

MOA2010-05_3C_sRNAomics_bioinformatics_PHAS-loci

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
...

  • MOA2010-05_3C_sRNAomics_bioinformatics_PHAS-loci.xlsx

MOA2010-05_3C_sRNAomics_bioinformatics_sRNA-targets-in-silico

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
...

  • MOA2010-05_3C_sRNAomics_bioinformatics_sRNA-targets-in-silico.xlsx

MOA2010-05_3C_sRNAomics_bioinformatics_sRNA-targets_miRNA-phasiRNA

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

  • MOA2010-05_3C_sRNAomics_bioinformatics_sRNA-targets_miRNA-phasiRNA.cys

MOA2010-05_3C_sRNAomics_bioinformatics_sRNA-targets_miRNA-phasiRNA-vsiRNA

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

  • MOA2010-05_3C_sRNAomics_bioinformatics_sRNA-targets_miRNA-phasiRNA-vsiRNA.cys

Degradomics

No description specified

MOA_Multiomics-Analysis_Phenodata-n-MIAPPE

Master table describing all the samples included in MOA Investigation; studies are descrubed using MIAPPE (Minimum Information About a Plant Phenotyping Experiment).

  • MOA_Multiomics-Analysis_Phenodata-n-MIAPPE.xlsx

MOA2010-05_4_degradomics_Degradome-Seq_GEO

Table connecting MOA degradome pool identifiers to GEO identifiers.

  • MOA2010-05_4_degradomics_Degradome-Seq_GEO.xlsx

MOA2010-05_4_degradomics_Degradome-Seq_targets-sRNA

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
...

  • MOA2010-05_4_degradomics_Degradome-Seq_targets-sRNA.xlsx

MOA2010-05_4_degradomics_Degradome-Seq_targets-vsiRNA

Targets of PVY-derived siRNAs identified by Degradome-Seq. For each predicted interaction, PVYNTN-derived siRNAs (vsiRNAs), 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 vsiRNA-target interaction, degradome category
...

  • MOA2010-05_4_degradomics_Degradome-Seq_targets-vsiRNA.xlsx

Proteomics

No description specified

MOA_Multiomics-Analysis_Phenodata-n-MIAPPE

Master table describing all the samples included in MOA Investigation; studies are descrubed using MIAPPE (Minimum Information About a Plant Phenotyping Experiment).

  • MOA_Multiomics-Analysis_Phenodata-n-MIAPPE.xlsx

MOA2010-05_5_proteomics_Orbitrap-MaxQuant

List of identified proteins and their counts; using MaxQuant software for selected MOA proteomics pool identifiers.

  • MOA2010-05_5_proteomics_Orbitrap-MaxQuant.xlsx

MOA2010-05_5_proteomics_Orbitrap-MaxQuant_peptides

List of identified peptides using MaxQuant software for selected MOA proteomics pool identifiers.

  • MOA2010-05_5_proteomics_Orbitrap-MaxQuant_peptides.xlsx

MOA2010-05_5_proteomics_Orbitrap-MaxQuant_logFC

Differentially expressed proteins between various comparison groups (Sheet: comparisons), with log2-fold changes and Benjamini-Hochberg FDR corrected p-values given for MaxQuant quantified proteins.

  • MOA2010-05_5_proteomics_Orbitrap-MaxQuant_logFC.xlsx

MOA2010-05_5_proteomics_Orbitrap-SpectralCounts

List of identified proteins and their counts; using spectral counts (Proteome Discoverer) for selected MOA proteomics pool identifiers.

  • MOA2010-05_5_proteomics_Orbitrap-SpectralCounts.xlsx

MOA2010-05_5_proteomics_Orbitrap-SpectralCounts_peptides

List of identified peptides using spectral counts (Proteome Discoverer) for selected MOA proteomics pool identifiers.

  • MOA2010-05_5_proteomics_Orbitrap-SpectralCounts_peptides.xlsx

MOA2010-05_5_proteomics_Orbitrap-SpectralCounts_logFC

Differentially expressed proteins between various comparison groups (Sheet: comparisons), with log2-fold changes and Benjamini-Hochberg FDR corrected p-values given for spectral count (Proteome Discoverer) quantified proteins.

  • MOA2010-05_5_proteomics_Orbitrap-SpectralCounts_logFC.xlsx

MOA2013-12

Hormonomics measurements.

Hormone concentrations

No description specified

MOA_Multiomics-Analysis_Phenodata-n-MIAPPE

Master table describing all the samples included in MOA Investigation; studies are descrubed using MIAPPE (Minimum Information About a Plant Phenotyping Experiment).

  • MOA_Multiomics-Analysis_Phenodata-n-MIAPPE.xlsx

MOA2013-12_1_hormonomics_GCMS

Concentrations of seven different plant hormones (ABA, GA3, OPDA, JA, IAA and SA) as determined by gas chromatography coupled with mass spectrometry (GC-MS) for MOA samples.

  • MOA2013-12_1_hormonomics_GCMS.xlsx

MOA2013-12_1_hormonomics_GCMS_ANOVA-groups

Significant changes for a set of hormones between treatment-genotype groups as determined by ANOVA followed by LSD post hoc analysis (FDR

  • MOA2013-12_1_hormonomics_GCMS_ANOVA-groups.xlsx

MOA2013-12_1_hormonomics_R-code

R code for the hormone analysis.

  • MOA2013-12_1_hormonomics_R-code.r
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Citation
Ramsak, Z., Stare, T., Križnik, M., & Gruden, K. (2019). MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection. FAIRDOMHub. http://doi.org/10.15490/fairdomhub.1.investigation.275.5
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Created: 30th Jul 2019 at 10:53

Last updated: 30th Jul 2019 at 10:53

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