Assays

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:

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 ...