Assays

Short Name: 02a_limmavoomDEbylines-R Assay Class: DRY Assay Type: R Title: DE of SxP RNA-seq data by lines Description: Data: total counts from mapping of SxPv1.0 reads to NbV1 genome; contrasting lines (low1-wt, low2-wt, high1-wt, high2-wt). pISA Assay creation date: 2020-02-12 pISA Assay creator: Mojca Juteršek Analyst: Mojca Juteršek Phenodata: ../../phenodata_20191104.xlsx Featuredata: Data:

Short Name: 03_NewGenome-MapMan Assay Class: DRY Assay Type: MapMan Title: MapMan visualisation of mapping SxP data to the new Nb genome Description: Data: logFC values of DE genes in SxPv1.0, MapMan3 mapping of NbV1 genome pISA Assay creation date: 2020-01-31 pISA Assay creator: Mojca Juteršek Phenodata: ../../phenodata_20181212.xlsx Featuredata: Data:

Short Name: 04_GSEA-Stat Assay Class: DRY Assay Type: Stat Title: GSEA analysis of SxP data Description: Gene sets: MapMan3 BINs from mapping of NbV1 genome, Data: TMM-normalized total counts of mapping SxPv1.0 data to NbV1 genome. pISA Assay creation date: 2020-01-31 pISA Assay creator: Mojca Juteršek Analyst: Mojca Juteršek Phenodata: ../../phenodata_20181212.xlsx Featuredata: Data:

Short Name: 05_Phenotype_analysis-Stat Assay Class: DRY Assay Type: Stat Title: Analysis of SxP phenotype Description: Plotting determined parameters: height, pheromone content, transgene expression. pISA Assay creation date: 2020-02-12 pISA Assay creator: Mojca Juteršek Analyst: Mojca Juteršek Phenodata: ../../phenodata_20191104.xlsx Featuredata: Data:

Short Name: 06_SxPv1-0_Illumina-Centrifuge Assay Class: DRY Assay Type: Centrifuge Title: centrifuge analysis of reads from SxPv1.0 samples Description: Centrifuge analysis of fastq files from SxPv1.0 samples to determine potential contaminations with pathogenic fungi, bacteria, that could potentially be behind the stress response observed in difeferntial expression analysis. pISA Assay creation date: 2021-10-21 pISA Assay creator: Mojca Juteršek Phenodata: ../../phenodata_20191104.txt Featuredata: ...

Short Name: 07_NbAUSv1-0-InterPro Assay Class: DRY Assay Type: InterPro Title: InterProScan annotation of the new Nb genome - NbAUSv1.0 Description: * pISA Assay creation date: 2021-10-21 pISA Assay creator: * Phenodata: ../../phenodata_20191104.txt Featuredata: Data:

Files connected to study: _S_P4_SxP10-newG-DE

Short Name: toNewGenome-CLC-mapping Assay Class: DRY Assay Type: CLC-mapping Title: Mapping of SxP RNA-seq to the new Nb genome Description: Data; SxPv1.0 RNA-Seq, genome: NbV1 pISA Assay creation date: 2020-01-31 pISA Assay creator: Mojca Juteršek Phenodata: ../../phenodata_20181212.xlsx Featuredata: Data:

Short Name: limmavoomDE-R Assay Class: DRY Assay Type: R Title: Differential expression analysis of SxP mapping to the new genome Description: Data: total counts from mapping of SxPv1.0 erads to the NbV1 genome. Contrasting high-low, high-wt, low-wt pISA Assay creation date: 2020-01-31 pISA Assay creator: Mojca Juteršek Analyst: Mojca Juteršek Phenodata: ../../phenodata_20181212.xlsx Featuredata: Data: