Assays

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 ...

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_GAtreat

Files connected to study: _S_P4_SxP10-newG-DE

Assay: AP4v10v12-phenotyping Short Name: P4v10v12-phenotyping Assay Class: WET Assay Type: phenotyping Title: Phenotyping of GA3 effect on SxP lines in comparison to wt Description: GA3 treated plants were followed for 35 days after transplanting in soil. Plant height was measured at 17, 21, 24, 28 and 35 days post planting in soil. At day 35 in soil, plants were collected, weighed and photographed for image analysis of leaf areas. The leaves and stems were dried and dry weigh measured. pISA Assay ...

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:

Files connected to study: _S_P4_DiNAR

Short Name: CKN-DiNAR Assay Class: DRY Assay Type: DiNAR Title: Visualisation of DE genes in SxPv1.0 lines with DiNAR Description: Mapping of SxPv1.0 data to Nb genome v1, DE was done by lines (low1, low2, high1, high2) against wt. pISA Assay creation date: 2020-12-15 pISA Assay creator: Mojca Juteršek Phenodata: None Featuredata: Data:

Short Name: CKN_NbL35-DiNAR Assay Class: DRY Assay Type: DiNAR Title: Visualisation of SxP DE genes in CKN with DiNAR tool Description: Mapping to Nb genome v3.5, DE was done by groups (v1.0 low, v1.0 high, v1.2 high) against wt and without the 3 outliers. pISA Assay creation date: 2022-01-30 pISA Assay creator: Mojca Juteršek Phenodata: None Featuredata: Data:

Short Name: PIS-DiNAR Assay Class: DRY Assay Type: DiNAR Title: SxP v1.0 DE genes visualised in DiNAR Description: Visualisation of DE genes from SxPv1.0 data in PIS network. Mapping to genome v1, contrasts by lines (low1, low2, high1, high2) pISA Assay creation date: 2020-12-15 pISA Assay creator: Mojca Juteršek Phenodata: None Featuredata: Data:

Short Name: PIS-SxPv12-DiNAR Assay Class: DRY Assay Type: DiNAR Title: SxP v1.2 DE genes visualised in DiNAR Description: Visualisation of DE genes from SxPv1.2 data in PIS network. Mapping to genome v1, contrasts by lines (low1, low2, high1, high2) pISA Assay creation date: 2021-11-10 pISA Assay creator: MJU Phenodata: ../../phenodata_20191104.txt Featuredata: Data:

Short Name: PIS_NbL35-DiNAR Assay Class: DRY Assay Type: DiNAR Title: DE genes of SxP v1.0 and v1.2 visualisation in DiNAR Description: As input, DE genes determined by contrasting phenotype groups without outliers were used. Mapping to Nb genome v3.5. Visualisatoin in PIS network. pISA Assay creation date: 2022-01-30 pISA Assay creator: Mojca Juteršek Phenodata: None Featuredata: Data:

Files connected to study: _S_P1_SxPv12T2

Files connected to study: _S_P4_CoExpNetViz

Short Name: SxPv10vsv12-phenotyping Assay Class: WET Assay Type: phenotyping Title: Images of phenotyping SxPv10, SxPv12 and WT for comparative study Description: Pictures taken of third generation of SPv10 plants, first generation of SxPv12 and WT before collecting samples pISA Assay creation date: 2021-11-25 pISA Assay creator: RMF Phenodata: ../../phenodata_20201212.txt Featuredata:

Short Name: SxPv12ScreeningT2-GCMS Assay Class: WET Assay Type: GCMS Title: Screening of sex pheromone production in SexyPlant v1.2 T2 transgenic generation for further RNASeq analysis. Description: The purpose of this study is to screen the population of T2 transgenic generation of SxPv1.2, to analyze the production of moth sex pheromones in these plants and be able to choose from them the most interesting ones in terms of production for further RNASeq analysis. pISA Assay creation date: 2021-12-09 ...

Short Name: 01_SxP_Data_Only-CoExp Assay Class: DRY Assay Type: CoExp Title: CoExpNetViz analysis using SUSPHIRE SxPv1.0 expression data only Description: CoExpNetViz analysis using SUSPHIRE SxPv1.0 expression data only - average logCPM values per line were used as inputs to generate coexpression network based on given baits. pISA Assay creation date: 2020-07-03 pISA Assay creator: Mojca Juteršek Phenodata: None Featuredata: Data:

Short Name: 02_Nb_datasets-CoExp Assay Class: DRY Assay Type: CoExp Title: CoExp analysis using available Nb RNA-seq datasets Description: CoExpNetViz analysis using SUSPHIRE SxPv1.0 expression data together with available RNA-Seq datsets from Nicotiana benthamiana - average logCPM values or clculated logFCs were used as inputs to generate coexpression networks based on given baits. pISA Assay creation date: 2020-07-03 pISA Assay creator: Mojca Juteršek Phenodata: None Featuredata: Data: