Data files
What is a Data file?Filters
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 ...
Creators: None
Submitter: Ziva Ramsak
sRNA regulatory network connecting endogenous miRNAs, phasiRNAs and their targets.
Creators: None
Submitter: Ziva Ramsak
sRNA regulatory network connecting miRNAs, phasiRNAs, PVY-derived siRNAs (vsiRNAs) and their targets.
Creators: None
Submitter: Ziva Ramsak
Table connecting MOA degradome pool identifiers to GEO identifiers.
Creators: None
Submitter: Ziva Ramsak
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 ...
Creators: None
Submitter: Ziva Ramsak
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 ...
Creators: None
Submitter: Ziva Ramsak
List of identified proteins and their counts; using MaxQuant software for selected MOA proteomics pool identifiers.
Creators: None
Submitter: Ziva Ramsak
List of identified peptides using MaxQuant software for selected MOA proteomics pool identifiers.
Creators: None
Submitter: Ziva Ramsak
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.
Creators: None
Submitter: Ziva Ramsak
List of identified proteins and their counts; using spectral counts (Proteome Discoverer) for selected MOA proteomics pool identifiers.
Creators: None
Submitter: Ziva Ramsak
List of identified peptides using spectral counts (Proteome Discoverer) for selected MOA proteomics pool identifiers.
Creators: None
Submitter: Ziva Ramsak
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.
Creators: None
Submitter: Ziva Ramsak
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.
Creators: None
Submitter: Ziva Ramsak
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.
Creators: None
Submitter: Ziva Ramsak
File describing the phenotypic observations taken on potato plants, namely spot necroses, vein necroses, chlorotic spots, yellowing and mechanicam damage.
Creators: None
Submitter: Ziva Ramsak
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).
Creators: None
Submitter: Ziva Ramsak
Statistical analysis of measurements of photosynthetic parameters.
Creators: None
Submitter: Ziva Ramsak
qPCR measured values of Potato virus Y (PVY).
Creators: None
Submitter: Ziva Ramsak
Table connecting MOA Investigation sample ID's and GEO sample identifiers.
Creators: None
Submitter: Ziva Ramsak
QC filtered and RSN normalised values for all MOA samples with microarray measurements.
Creators: None
Submitter: Ziva Ramsak
Differential expression of genes between various comparison groups (Sheet: comparisons), with log2-fold changes and Benjamini-Hochberg FDR corrected p-values given.
Creators: None
Submitter: Ziva Ramsak
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).
Creators: None
Submitter: Ziva Ramsak
RT-qPCR assays for microarray validation described using the MIQE standard.
Creators: None
Submitter: Ziva Ramsak
Table connecting MOA sample identifiers to GEO identifiers related to sRNAomics dataset.
Creators: None
Submitter: Ziva Ramsak
miRNAs and their counts identified in the MOA samples for sRNA-Seq.
Creators: None
Submitter: Ziva Ramsak
miRNAs and their RPM normalised counts identified in the MOA samples for sRNA-Seq.
Creators: None
Submitter: Ziva Ramsak
Differential expression of miRNAs between various comparison groups (Sheet: comparisons), with log2-fold changes and Benjamini-Hochberg FDR corrected p-values given.
Creators: None
Submitter: Ziva Ramsak
Here published artikel about The FAIR Guiding Principles for scientific data management and stewardship
Creators: None
Submitter: Olga Krebs
FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq
Creators: Fabian Grammes, Yang Jin
Submitter: Sahar Hassani
FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq
Creators: Fabian Grammes, Yang Jin
Submitter: Sahar Hassani