Assays

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:

Files connected to study: _S_P1_SxPAltAcTransferases

Files connected to study: _S_P1_SxPv10vsSxP12

Short Name: SxPAlternativeAcetyltransferases-GCMS Assay Class: WET Assay Type: GCMS Title: Assay of transient expression of alternative acetyltransferases Description: The purpose of this assay is to test the efficiency of conversion of Z11-16OH to Z11-16OAc, in the search of a more efficient alternative to the already used EaDact acetyltransferase gene, chosen for the generation of the SxPv10 and SxPv12. The expression is assayed in a transient expression assay on WT Nicotiana benthamiana plants, ...

Short Name: LeavesSxPv10vsv12-GCMS Assay Class: WET Assay Type: GCMS Title: Leaf volatilome of SxPv1.0, SxPv1.2 T1 and WT Description: The purpose of this assay is to define the volatilome of SxPv1.0, v1.2 and WT Nicotiana benthamiana plant leaves, focusing on the differences between them, by GC-MS. pISA Assay creation date: 2020-12-12 pISA Assay creator: RMF Lab manager: DO Sample collection protocol: Leaf samples were collected at 4 weeks after transplant for young stage and at 7 weeks for adult ...

Short Name: RootsSxPv10vsv12-GCMS Assay Class: WET Assay Type: GCMS Title: Roots volatilome of SxPv1.0, SxPv1.2 T1 and WT Description: The purpose of this assay is to define the volatilome of SxPv1.0, v1.2 and WT Nicotiana benthamiana plant roots, focusing on the differences between them, by GC-MS. pISA Assay creation date: 2021-11-25 pISA Assay creator: RMF Lab manager: DO Sample collection protocol: Root samples were collected at 7 weeks, in a early flowering stage of plants. Samples were ...

Files connected to study: _S_P1_SPv1TransientExp

Short Name: SPv10_phenotyping-Images Assay Class: WET Assay Type: Images Title: Images of SPv1 T2 and T3 plants Description: Photographs taken of second and third generations of SPv1.0 plants before collecting samples pISA Assay creation date: 2018-11-19 pISA Assay creator: ElenaMG Phenodata: ../../phenodata_20200416.txt Featuredata:

Short Name: SPv10T2Analysis-GCMS Assay Class: WET Assay Type: GCMS Title: Analysis of SPv1.0 T2 plants Description: Analysis of pheromone content in T2 generation of SPv1.0 plants pISA Assay creation date: 2021-11-01 pISA Assay creator: ElenaMG Lab manager: DO Sample collection protocol: Leaf samples were collected at 4 weeks after transplant for young stage and at 7 weeks for adult stage (early flowering). Samples were collected between 4 and 6 pm, frozen in liquid nitrogen immediately after ...

Assay: ASPv10T3Analysis-GCMS Short Name: SPv10T3Analysis-GCMS Assay Class: WET Assay Type: GCMS Title: Analysis of SPv1.0 T3 plants Description: Analysis of pheromone content in T3 generation of SPv1.0 plants pISA Assay creation date: 2021-11-01 pISA Assay creator: ElenaMG Lab manager: DO Sample collection protocol: Leaf samples were collected at 4 weeks after transplant for young stage and at 7 weeks for adult stage (early flowering). Samples were collected between 4 and 6 pm, frozen in liquid ...

Short Name: SPv10EaDActAnalysis-GCMS Assay Class: WET Assay Type: GCMS Title: Transient expression in Nicotiana benthamiana leaves of the moth pheromone pathway with and without EaDAct Description: The effect of EaDAct in pheromone production was studied by agroinfiltrating in Nicotiana benthamiana leaves the first two enzymes (AtrD11 and HarFAR) with or without the last enzyme EaDAct. P19 was also agroinfiltrated as negative control. pISA Assay creation date: 2019-12-08 pISA Assay creator: ElenaMG ...

Short Name: TransientSPv11andSPv12-GCMS Assay Class: WET Assay Type: GCMS Title: Transient expression of constructs for SxPv1.1 and SxPv1.2 Description: The constructs for SxPv1.1 and SxPv1.2 were tested transiently in Nicotiana benthamiana leaves. Pheromone content was analysed via GC-MS pISA Assay creation date: 2020-07-23 pISA Assay creator: ElenaMG Lab manager: DO Sample collection protocol: Leaf samples were collected at 4 weeks after transplant for young stage and at 7 weeks for adult stage ...

Files connected to investigation: _I_T21_SXPsysbio

Files connected to study: _S_P1_SPv10T0andT1

Files connected to study: _S_P1_SPv10T2andT3

Short Name: SP10T0Analysis-GCMS Assay Class: WET Assay Type: GCMS Title: Analysis of SPv1.0 T0 plants Description: Stable transformation of Nicotiana benthamiana plants with the three enzymes for moth pheromone production (AtrD11, HarFAR, EaDAct) expressed constitutively pISA Assay creation date: 2021-11-01 pISA Assay creator: ElenaMG Lab manager: DO Sample collection protocol: Leaf samples were collected at 4 weeks after transplant for young stage and at 7 weeks for adult stage (early flowering). ...

Short Name: SP10T1Analysis-GCMS Assay Class: WET Assay Type: GCMS Title: Analysis of SPv1.0 T1 plants Description: Analysis of pheromone content in T1 generation of SPv1.0 plants pISA Assay creation date: 2021-11-01 pISA Assay creator: ElenaMG Lab manager: DO Sample collection protocol: Leaf samples were collected at 4 weeks after transplant for young stage and at 7 weeks for adult stage (early flowering). Samples were collected between 4 and 6 pm, frozen in liquid nitrogen immediately after ...

Liver samples from Atlantic cod males. Total RNA isolated using TRI Reagent (Fekadu Yadetie). Sequencing performed with Illumina Stranded mRNA (sequencing poly-A mRNA) at Genomic Core Facility at UiB/Haukeland (contact person Rita Holdhus).

The data sets are submitted to the ArrayExpress repository, and will be linked here.

Untargeted lipidomics analysis was performed on plasma and liver samples of four male fish from each group (n = 4) at Per Bruheim’s lab at NTNU, Norway, using Liquid Chromatography Hybrid Quadrupole Mass Spectrometry (UPLC-HDMS).

Dear SEEK users, this Assay is just an example Excel sheet for intracellular metabolites concentration measurements performed using cell culture growing in chemostat

From the "data accessibility" section of Life-stage associated remodeling of lipid metabolism regulation in Atlantic salmon. (Publication):

Supplementary files have been deposited to datadryad.org under the accession: https://doi.org/10.5061/dryad.j4h65. Raw RNA-Seq data have been deposited into European Nucleotide Archive (ENA) under the project Accession no. PRJEB24480.

Dead links 2022-06-29 (the Shiny ...