Data files

LFQ intensities derived from proteomics measurements

Information for RNA and protein samples and cultures they were derived from.

TPM counts for protein coding genes, alongside functional annotations

Source code for running simulations

Archive contains python scripts for image analysis

Images used for training and validation of deep learning algorithm to determine biofilm composition of mixed species biofilms on mineral grains

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

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

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.

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

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.

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

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

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.

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

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.

Significant changes for a set of hormones between treatment-genotype groups as determined by ANOVA followed by LSD post hoc analysis (FDR < 0.05) using the Agricolae R package.