Assays

Harvest optical densites and methods of transcriptom, proteom and metabolom samples for all tested substrat conditions.

All flux balance analyses of the stoichiometric model

All files for metabolic modeling using the Metano toolbox, including the scenarios and flux balance analyses.

Assay: ASxPv12limmavoomDE-R Short Name: SxPv12limmavoomDE-R Assay Class: DRY Assay Type: R Title: Differential expression analysis of SxPv1.2 data in R Description: Difefrential expression analysis with limma-voom sript in R of total counts from mapping of SxPv1.2 reads to the NbV1 genome. pISA Assay creation date: 2021-11-10 pISA Assay creator: Mojca Juteršek Analyst: Mojca Juteršek Phenodata: ../../phenodata20191104.txt Featuredata: Data:

Short Name: 04_SxPv12_GeneSetEnrichment-RNAseg-GSEA Assay Class: DRY Assay Type: RNAseq-GSEA Title: GSEA of SxPv1.2 expression data Description: GSEA anaylysis with MapMan3 BINs as gene sets and SxPv1.2 logFC data. pISA Assay creation date: 2021-11-24 pISA Assay creator: Mojca Juteršek Phenodata: ../../phenodata_20191104.txt Featuredata: Data:

Files connected to study: _S_P4_SxP12-newG-DE

Short Name: 03_MapMan-visualisation Assay Class: DRY Assay Type: visualisation Title: Visualisation of DE SxP genes in MapMan. MapMan3 mapping as input. pISA Assay creation date: 2021-12-31 pISA Assay creator: Mojca Jutersek Phenodata: None Featuredata: Data:

Short Name: 04_MapManBINenrich-GSEA Assay Class: DRY Assay Type: GSEA Title: GSEA for SxP Illumina mapped reads Description: GSEA of TMM normalized total counts from mapping of SxP Illumina reads to Nb genome v3.5 pISA Assay creation date: 2021-12-31 pISA Assay creator: Mojca Jutersek Phenodata: None Featuredata: Data:

Short Name: 05_VOCcomp-Bioinfo Assay Class: DRY Assay Type: Bioinfo Title: Analysis of VOC data from SxP v1.0 and v1.2 and its comparison to transcriptomic data. Description: Volatile organic compound analysis of young and adult v1.0 and v1.2 high producers was compared to transcriptomic data to gain more insight into the metabolic perturbations in SxP producers. pISA Assay creation date: 2022-01-19 pISA Assay creator: Mojca Jutersek Phenodata: None Featuredata: Data:

Short Name: SxPv1-2_fastq-QC Assay Class: DRY Assay Type: QC Title: Qulaity control of SxPv1-2 raw Illumina reads Description: FastQC of SxPv1.2 Illumina reads pISA Assay creation date: 2021-11-08 pISA Assay creator: Mojca Juteršek Phenodata: ../../phenodata_20191104.txt Featuredata: Data:

Short Name: SxPv12_mapping-CLC Assay Class: DRY Assay Type: CLC Title: CLC mapping of SxPv1.2 reads Description: Mapping SxPv1.2 Illumina reads to NbV1 genome in CLC Genomics Workbench pISA Assay creation date: 2021-11-10 pISA Assay creator: Mojca Juteršek Phenodata: ../../phenodata_20191104.txt Featuredata: Data:

Files connected to study: _S_P4_SxP1012-finalG

Short Name: 06_MapMan-bioinfo Assay Class: DRY Assay Type: bioinfo Title: MapMan visualisation of DE genes in SxP Description: LogFCs from DE analysis of total counts after mapping with CLC and Mercator3 mapping as inputs. pISA Assay creation date: 2019-03-27 pISA Assay creator: Mojca Juteršek Phenodata: ../../phenodata_20181212.xlsx Featuredata: Data:

Short Name: 08_transgenes-CLC Assay Class: DRY Assay Type: CLC Title: Mapping of RNA-seq data from SxP to transgenes Description: Mapping SxPv1.0 RNA-Seq reads to seqeunces of the three transgenes to determine transgene expression. pISA Assay creation date: 2019-07-09 pISA Assay creator: Mojca Juteršek Featuredata: Data:

Short Name: 01_mapping-CLC Assay Class: DRY Assay Type: CLC Title: Mapping of SxP v1.0 and v1.2 Illumina reads to V3.5 Nb genome Description: Mapping of SxP v1.0 and v1.2 Illumina reads to V3.5 Nb genome in CLC Genomics Workbench. pISA Assay creation date: 2021-12-20 pISA Assay creator: Mojca Jutersek Phenodata: None Featuredata: Data:

Short Name: 02a_limmavoom-multim-R Assay Class: DRY Assay Type: R Title: limmavoom DE analysis of multimapped SxP Illumina reads Description: DE analysis with limma-voom script in R of total count data from mapping of SxPv1.0 and v1.2 reads to NbV3.5 genome and counting multimapped reads. pISA Assay creation date: 2021-12-30 pISA Assay creator: Mojca Jutersek Analyst: Mojca Jutersek Phenodata: None Featuredata: Data:

Short Name: 02b_limmavoom-uniquem-R Assay Class: DRY Assay Type: R Title: Limmavoom DE analysis of uniquely mapped SxP Illumina reads Description: DE analysis with limma-voom script in R of total count data from mapping of SxPv1.0 and v1.2 reads to NbV3.5 genome and counting only uniquely mapped reads. pISA Assay creation date: 2021-12-30 pISA Assay creator: Mojca Jutersek Analyst: Mojca Jutersek Phenodata: None Featuredata: Data:

Assay: A02FastQC-bioinfo Short Name: 02FastQC-bioinfo Assay Class: DRY Assay Type: bioinfo Title: QC of raw reads Description: FastQ analysis of raw reads from SxPv1.0 RNA-Seq samples. pISA Assay creation date: 2019-03-20 pISA Assay creator: Mojca Juteršek Phenodata: ../../phenodata20181212.xlsx Featuredata: Data: __

Short Name: 03_mapping-CLC Assay Class: DRY Assay Type: CLC Title: 03_CLCmapping Description: Mapping of SxPv1.0 reads to the Kourelis 2019 Nb genome with CLC Genomics Workbench. pISA Assay creation date: 2019-26-03 pISA Assay creator: Mojca Juteršek Phenodata: ../../phenodata_20181212.xlsx Featuredata: Data:

Short Name: 03a_mapping2-STAR Assay Class: DRY Assay Type: STAR Title: Mapping of SxP reads with STAR Description: Mapping of SxPv1.0 reads to the Kourelis 2019 Nb genome with STAR. pISA Assay creation date: 2019-04-19 pISA Assay creator: Mojca Juteršek Phenodata: ../../phenodata_20181212.xlsx Featuredata: Data:

Short Name: 04_Mercator-bioinfo Assay Class: DRY Assay Type: bioinfo Title: Mercator annotation of Nbenthamiana fasta file Description: Mercator3 annotation of Kourelis 2019 Nb genome pISA Assay creation date: 2019-04-09 pISA Assay creator: Mojca Juteršek Phenodata: ../../phenodata_20181212.xlsx Featuredata: Data:

Assay: A05DEstat-R Short Name: 05DEstat-R Assay Class: DRY Assay Type: R Title: Analysis of DE genes in R limma voom Description: DE analysis of SxPv1.0 count data with total counts determined from mapping with CLC. pISA Assay creation date: 2019-03-27 pISA Assay creator: Mojca Juteršek Analyst: Mojca Juteršek Phenodata: ../../phenodata20181212.xlsx Featuredata: Data:

Short Name: 05a_DEstat2-R Assay Class: DRY Assay Type: R Title: DE analysis in R with count data from STAR Description: DE analysis of SxPv1.0 count data with total counts determined from mapping with STAR. pISA Assay creation date: 2019-04-19 pISA Assay creator: Mojca Juteršek Analyst: Marko Petek Phenodata: ../../phenodata_20181212.xlsx Featuredata: Data:

Short Name: 05b_DElow-wt-R Assay Class: DRY Assay Type: R Title: DE analysis in R using low-wt contrast Description: DE with total counts from mapping with CLC, contrasting low producers to wt. pISA Assay creation date: 2019-09-18 pISA Assay creator: Mojca Juteršek Analyst: Mojca Juteršek Phenodata: ../../phenodata_20181212.xlsx Featuredata: Data:

Files connected to study: _S_P4_SxP10-oldG-DE

Short Name: 00_SxP_photos-phenotyping Assay Class: WET Assay Type: phenotyping Description: Photos of SxPv1.0 plants grown in greenhouse in Valencia (IBMCP) for RNA-Seq sampling. pISA Assay creation date: 2018-11-09 pISA Assay creator: Mojca Juteršek Phenodata: ../../phenodata_20181212.xlsx Featuredata: Data:

Assay: _A_01_RNA1-RNAisol Short Name: RNA1-RNAisol Assay Class: WET Assay Type: RNAisol Title: RNA isolation from sexy plants Description: Isolation of RNA from SxPv1.0 plants. 4 biological replicates per every included line. pISA Assay creation date: 2018-12-13 pISA Assay creator: SpelaB Lab manager: Elena Phenodata: None Featuredata: Creation date: 2018-12-13 RNA ID: $_RNA Homogenisation protocol: fastPrep Date Homogenisation: 2018-12-13 Isolation Protocol: Rneasy_Plant Date Isolation: 2018-12-13 ...