Data files

Code used for the analysis of microarray data.

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

Data file for PLaSMo accesssion ID PLM_74, version 1

Data file for PLaSMo accesssion ID PLM_74, version 1

Data file for PLaSMo accesssion ID PLM_74, version 1

Data file for PLaSMo accesssion ID PLM_75, version 1

Data file for PLaSMo accesssion ID PLM_76, version 1

Data file for PLaSMo accesssion ID PLM_76, version 1

Data file for PLaSMo accesssion ID PLM_73, version 1

TPM counts for protein coding genes, alongside functional annotations

LFQ intensities derived from proteomics measurements

Source code for running simulations

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

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

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.