Assays

What is an Assay?
978 Assays visible to you, out of a total of 1941

Short Name: 00_Ecoli-dry Assay Class: DRY Assay Type: dry Title: E coli HT115 data Description: Information on E coli bacteria used for dsRNA production pISA Assay creation date: 2021-01-14 pISA Assay creator: Marko Petek Phenodata: None Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_03_dsRNAprod

Short Name: 00_jun2017_dsRNA_stabil-wet Assay Class: WET Assay Type: wet Title: Stability testing of in-vitro synthetised dsRNA Description: Stability testing by gel electrophoresis before/after DNase and RNase reactions pISA Assay creation date: 2021-05-10 pISA Assay creator: Marko Petek Phenodata: None Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_09_jun2017

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:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_SxP10-oldG-DE

Short Name: 01_AgroRNA-wet Assay Class: WET Assay Type: wet Title: Order dsRNA in-vitro synthesis at AgroRNA Description: Materials associated with the order of in-vitro synthesis of designed dsRNA, results of cleaning procedure and DNase I test to ensure the material is not DNA pISA Assay creation date: 2021-01-14 pISA Assay creator: Marko Petek Phenodata: None Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_02_dsRNAorder

Short Name: 01_dec2016-phenotyping Assay Class: WET Assay Type: phenotyping Title: Measuring feeding trial parameters Description: Weight gain, survival, photos and other phenotypic observations pISA Assay creation date: 2021-05-10 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210113.txt Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_07_dec2016

Assay: _A_01_evigene Short Name: 01_evigene Assay Class: DRY Assay Type: evigene Title: EvidentialGene tr2aacds.pl VERSION 2016.07.11 Description: See http://eugenes.org/EvidentialGene/about/EvidentialGene_trassembly_pipe.html pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt

Short Name: 01_GC_content-count Assay Class: DRY Assay Type: count Title: GC content and sequence length Description: A, C, T, G content and sequence length pISA Assay creation date: 2020-03-09 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data: ../input/path_to_files.txt

Short Name: 01_jan2017-phenotyping Assay Class: WET Assay Type: phenotyping Title: Measuring feeding trial parameters Description: Weight gain, survival, photos and other phenotypic observations pISA Assay creation date: 2021-05-10 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210113.txt Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_08_jan2017

Short Name: 01_jun19-wet Assay Class: WET Assay Type: wet Title: June 2019 potato field trial Description: June 2019 potato field trial conducted as part of Ecobreed project from KIS coordinated by dr. Jaka Razinger pISA Assay creation date: 2021-01-15 pISA Assay creator: Marko Petek Phenodata: None Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_02_FieldTrials

Study: _S_01_2019

Short Name: 01_jun20-wet Assay Class: WET Assay Type: wet Title: June 2020 potato field trial Description: June 2020 potato field trial conducted as part of Ecobreed project from KIS coordinated by dr. Jaka Razinger pISA Assay creation date: 2021-01-15 pISA Assay creator: Marko Petek Phenodata: None Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_02_FieldTrials

Study: _S_02_2020

Short Name: 01_jun2016-phenotyping Assay Class: WET Assay Type: phenotyping Title: Measuring feeding trial parameters Description: Weight gain, survival, photos and other phenotypic observations pISA Assay creation date: 2021-05-10 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210113.txt Featuredata: Data:

Short Name: 01_jun2017-phenotyping Assay Class: WET Assay Type: phenotyping Title: Measuring feeding trial parameters Description: Weight gain, survival, photos and other phenotypic observations pISA Assay creation date: 2021-05-10 pISA Assay creator: Marko Petek, Valentina Levak Phenodata: ../../phenodata_20210113.txt Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_09_jun2017

Short Name: 01_jun2017-phenotyping Assay Class: WET Assay Type: phenotyping Title: Measuring feeding trial parameters (using dsRNA produced in vivo in E coli) Description: Weight gain, survival, photos and other phenotypic observations pISA Assay creation date: 2021-05-10 pISA Assay creator: Marko Petek, Rok Ferenc Phenodata: ../../phenodata_20210113.txt Featuredata: Data:

Short Name: 01_LitData-dry Assay Class: DRY Assay Type: dry Title: Compiling literature data on RNAi screens in insects Description: Compiling articles and final results of insect RNAi screens in model organisms (e.g. Drosophila melanogaster, Tribolium castaneum) pISA Assay creation date: 2021-01-13 pISA Assay creator: Marko Petek Phenodata: None 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: 01_may2018-phenotyping Assay Class: WET Assay Type: phenotyping Title: Measuring feeding trial parameters Description: Hatching, weight gain, survival, photos and other phenotypic observations pISA Assay creation date: 2021-05-10 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210113.txt Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_11_may2018

Short Name: 01_oct2016-phenotyping Assay Class: WET Assay Type: phenotyping Title: Measuring feeding trial parameters Description: Weight gain, survival, photos and other phenotypic observations pISA Assay creation date: 2021-05-10 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210113.txt Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_06_oct2016

Short Name: 01_pIsol-wet Assay Class: WET Assay Type: wet Title: Plasmid isolation from bacterial culture Description: Plasmids were obtained as bacterial culture from Addgene and isolated to be used for cloning pISA Assay creation date: 2021-01-14 pISA Assay creator: Marko Petek Phenodata: None Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_03_dsRNAprod

Short Name: 01_RNA-Seq_dsEGFP-NGS Assay Class: WET Assay Type: NGS Title: Treatment of dsEGFP and water treated samples before sending for RNA-Seq Description: RNA-Seq DNase and cleanup of dsEGFP and water treated CPB larval samples from the june2017 experiment to determine non-specific response of dsRNA consumption pISA Assay creation date: 2021-05-10 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210115.txt Featuredata:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_03_Omics

Study: _S_01_ns-dsRNA_trans

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 ...

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_SxP10-oldG-DE

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: 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:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_SxP12-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:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_SxP10-newG-DE

Short Name: 01-DNAisol Assay Class: WET Assay Type: DNAisol Title: Isolation of gDNA from CPB gut content Description: Isolation of gDNA from CPB gut content pISA Assay creation date: 2021-01-15 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210115.txt Featuredata: Data:

Short Name: cdhit_3cvs-GFFmerged Assay Class: DRY Assay Type: GFFmerged Title: cdhit-est and cdhit-2d on 3cv and ITAG/PGSC Description: cdhit-est and cdhit-2d on 3cv and ITAG/PGSC pISA Assay creation date: 2020-03-09 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT

Study: _S_04_stPanTr

Short Name: 02_CLC-RNASeq Assay Class: DRY Assay Type: RNASeq Title: CLC RNA-Seq data analysis dsEGFP vs water treatment Description: CLC RNA-Seq data analysis dsEGFP vs water treatment pISA Assay creation date: 2021-05-10 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210115.txt Featuredata: Data:

Short Name: 02_dec2016-RNAisol Assay Class: WET Assay Type: RNAisol Title: RNA isolation and pre-qPCR sample prep Description: RNA isolation and sample preparation for qPCR pISA Assay creation date: 2021-05-10 pISA Assay creator: Marko Petek Lab manager: Marko Petek Phenodata: ../../phenodata_20210113.txt Featuredata: RNA ID: $_RNA Homogenisation protocol: handheld electric rotor-stator homogenization in tubes with Trizol Date Homogenisation: 2017-08-17 Isolation Protocol: ZymoRNA Date Isolation: ...

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: __

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_SxP10-oldG-DE

Short Name: 02_jun2016-RNAisol Assay Class: WET Assay Type: RNAisol Title: RNA isolation and pre-qPCR sample prep Description: RNA isolation and sample preparation for qPCR pISA Assay creation date: 2021-05-10 pISA Assay creator: Marko Petek Lab manager: Marko Petek Phenodata: ../../phenodata_20210113.txt Featuredata: RNA ID: $_RNA Homogenisation protocol: handheld electric rotor-stator homogenization in tubes with Trizol Date Homogenisation: 2017-04-26 Isolation Protocol: ZymoRNA Date Isolation: ...

Short Name: 02_jun2017-RNAisol Assay Class: WET Assay Type: RNAisol Title: RNA isolation and pre-qPCR sample prep Description: RNA isolation and sample preparation for qPCR pISA Assay creation date: 2021-05-10 pISA Assay creator: Marko Petek Lab manager: Marko Petek Phenodata: ../../phenodata_20210113.txt Featuredata: RNA ID: $_RNA Homogenisation protocol: handheld electric rotor-stator homogenization in tubes with Trizol Date Homogenisation: 2017-07-17 Isolation Protocol: ZymoRNA Date Isolation: ...

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:

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:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_CoExpNetViz

Short Name: 02_plasmid-SangerSeq Assay Class: WET Assay Type: SangerSeq Title: Sanger sequencing of Addgene plasmids Description: Sanger sequencing of Addgene plasmids pISA Assay creation date: 2021-01-14 pISA Assay creator: Marko Petek Phenodata: None Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_03_dsRNAprod

Short Name: 02_qPCR_ampl_test-wet Assay Class: WET Assay Type: wet Title: Test of qPCR amplicons Description: Test of qPCR ampliconed designed to follow expression of target genes pISA Assay creation date: 2021-05-10 pISA Assay creator: Marko Petek Phenodata: None 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:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_SxP12-newG-DE

Short Name: 02_UlrichTop100-BLAST Assay Class: DRY Assay Type: BLAST Title: BLAST Ulrich top100 hits from Tribolium against CPB Description: Analysis of BLAST results from a query of top100 differentially expressed genes of Tribolium castaneum against Colorado potato beetle transcripts pISA Assay creation date: 2021-01-13 pISA Assay creator: Marko Petek Phenodata: None Featuredata: Data:

Short Name: 02-DNASeq Assay Class: WET Assay Type: DNASeq Title: Shotgun CPB gut microbiome DNA-Seq Description: Sequencing of CPB gut microbiome genomic DNA to determine the offect of dsRNA feeding on the microbial flora pISA Assay creation date: 2021-01-15 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210115.txt Featuredata:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_03_Omics

Study: _S_02_metagenome_resp

Assay: _A_02.1_BUSCO Short Name: 02.1_BUSCO Assay Class: DRY Assay Type: BUSCO Title: BUSCO on assemblies and tr2aacds output Description: BUSCO on assemblies and tr2aacds output pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt

Submitter: Maja Zagorscak

Biological problem addressed: Validation

Investigation: _I_STRT

Study: _S_03_stCuSTr

Assay: _A_02.2_assembly-contribution-count Short Name: 02.2_assembly-contribution-count Assay Class: DRY Assay Type: count Title: assembly contribution count Description: assembly contribution count, input/output tr2aacds pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt

Assay: _A_02.3_InterProScan Short Name: 02.3_InterProScan Assay Class: DRY Assay Type: InterProScan Title: InterProScan on tr2aacds output Description: InterProScan on tr2aacds output pISA Assay creation date: 2019-10-22 pISA Assay creator: Marko Petek Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt

Assay: _A_02.4_STAR Short Name: 02.4_STAR Assay Class: DRY Assay Type: STAR Title: mapping reads back to evigene .tr output Description: mapping reads back to evigene .tr output using STAR to check the percentage of reads that map pISA Assay creation date: 2019-10-22 pISA Assay creator: Marko Petek Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt

Assay: _A_02.5_STARlong_matchAnnot Short Name: 02.5_STARlong_matchAnnot Assay Class: DRY Assay Type: matchAnnot Title: potato transcriptome v2 (evigene) STARlong mapping of transcripts to reference genome and MatchAnnot to get transcript annotations Description: potato initial transcriptome (evigene) STARlong mapping of transcripts to reference genome and MatchAnnot to get transcript annotations pISA Assay creation date: 2019-10-22 pISA Assay creator: Marko Petek Phenodata: None Featuredata: None ...

Assay: _A_02.6_TransRate Short Name: 02.6_TransRate Assay Class: DRY Assay Type: TransRate Title: TransRate stat on raw tr2aacds transcriptomes Description: TransRate stat on raw (initial) tr2aacds transcriptomes, basic and reference-based pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Nonde Data: see ./input/path_to_files.txt

Submitter: Maja Zagorscak

Biological problem addressed: Validation

Investigation: _I_STRT

Study: _S_03_stCuSTr

Assay: _A_02.7_VecScreen Short Name: 02.7_VecScreen Assay Class: DRY Assay Type: VecScreen Title: VecScreen on raw tr2aacds output Description: VecScreen (contamination screening) and blastn (contaminants annotation) on raw (initial) tr2aacds output pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt

Assay: _A_02.8_DIAMOND Short Name: 02.8_DIAMOND Assay Class: DRY Assay Type: DIAMOND Title: DIAMOND on raw tr2aacds output Description: DIAMOND on raw tr2aacds output, both .cds and .tr; including lost and found pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt

Submitter: Maja Zagorscak

Biological problem addressed: Annotation

Investigation: _I_STRT

Study: _S_03_stCuSTr

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: 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:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_SxP10-newG-DE

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:

Short Name: 03_components_3cvs-GFFmerged Assay Class: DRY Assay Type: GFFmerged Title: components Description: representative and alternative pan-transcriptome CDS and polypeptide fasta files pISA Assay creation date: 2020-03-10 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT

Study: _S_04_stPanTr

Short Name: 03_dec2016-qPCR Assay Class: WET Assay Type: qPCR Title: qPCR for target genes Description: Quantitative PCR (qPCR) for selected target genes using the established methodology at NIB. pISA Assay creation date: 2021-05-10 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210113.txt Featuredata: Data: Lab manager: Kristina Gruden Assay chemistry: mixed Assay optimisation protocol (file path, link or citation): Pippeting: liquid handling station Reaction volume: 5 ul qPCR ...

Short Name: 03_jun2016-qPCR Assay Class: WET Assay Type: qPCR Title: qPCR for target genes Description: Quantitative PCR (qPCR) for selected target genes using the established methodology at NIB. pISA Assay creation date: 2021-05-10 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210113.txt Featuredata: Data: ../../_S_07_dec2016/_A_03-qPCR/output Lab manager: Kristina Gruden Assay chemistry: mixed Assay optimisation protocol (file path, link or citation): Pippeting: liquid handling ...

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_05_jun2016

Short Name: 03_jun2017-qPCR Assay Class: WET Assay Type: qPCR Title: qPCR for target genes Description: Quantitative PCR (qPCR) for selected target genes using the established methodology at NIB. pISA Assay creation date: 2021-05-10 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210113.txt Featuredata: Data: Lab manager: Kristina Gruden Assay chemistry: mixed Assay optimisation protocol (file path, link or citation): Pippeting: liquid handling station Reaction volume: 5 ul qPCR ...

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: 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:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_SxP10-oldG-DE

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: 03_patentDB-BLAST Assay Class: DRY Assay Type: BLAST Title: NCBI patent BLAST Description: This is to find CPB nucleotide and peptide sequences that are already protected by patents pISA Assay creation date: 2021-01-14 pISA Assay creator: Marko Petek Phenodata: None Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_01_TargetSelect

Short Name: 03_RNaseItreat-wet Assay Class: WET Assay Type: wet Title: RNase If treatment of dsRNA Description: RNase If treatment of dsRNA produced in-vivo pISA Assay creation date: 2021-01-14 pISA Assay creator: Marko Petek Phenodata: None Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_03_dsRNAprod

Short Name: 03_stages-RNAisol Assay Class: WET Assay Type: RNAisol Title: Expression of target genes in CPB developmental stages and body parts Description: Expression of target genes in CPB developmental stages and body parts - RNA isolation pISA Assay creation date: 2021-05-10 pISA Assay creator: Marko Petek Lab manager: Marko Petek Phenodata: ../../phenodata_20210113.txt Featuredata: RNA ID: $_RNA Homogenisation protocol: handheld electric rotor-stator homogenization in tubes with Trizol Date ...

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:

Assay: _A_03.1_filtering Short Name: 03.1_filtering Assay Class: DRY Assay Type: filtering Title: Filtering according to biological evidence; removal of contaminants, chimeras and suspicious constructs Description: Filtering according to biological evidence; removal of contaminants, chimeras and suspicious constructs pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt

Assay: _A_03.2_components Short Name: 03.2_components Assay Class: DRY Assay Type: components Title: Components: tr2aacds headers, cdhit-2d Description: Components: tr2aacds headers, cdhit-2d; post-filtering redefinition of paralogue clusters pISA Assay creation date: 2019-10-22 pISA Assay creator: Ziva Ramsak Phenodata: None Featuredata: Data:

Submitter: Maja Zagorscak

Biological problem addressed: Annotation

Investigation: _I_STRT

Study: _S_03_stCuSTr

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_BUSCO_3cvs-GFFmerged Assay Class: DRY Assay Type: GFFmerged Title: BUSCOs Description: BUSCO on ITAG, PGSC, ITAG/PGSC merged, pan-transcriptome representatives, pan-transcriptome alternatives, and pan-transcriptome pISA Assay creation date: 2020-03-10 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:

Short Name: 04_DE_divers-R Assay Class: DRY Assay Type: R Title: Diversity analysis and differential abundance Description: Metagenomic diversity analyisis using kraken data in R and differential abundance using phyloseq and DESeq R packages. pISA Assay creation date: 2021-01-15 pISA Assay creator: Marko Petek Analyst: Marko Petek Phenodata: ../../phenodata_20210115.txt 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: 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:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_SxP1012-finalG

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:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_SxP10-oldG-DE

Short Name: 04_ortho-BLAST Assay Class: DRY Assay Type: BLAST Title: BLAST to determine orthologs to model organisms Description: BLAST against D melanogaster and T castaneum to identify putative orthologous genes of CPB pISA Assay creation date: 2021-01-14 pISA Assay creator: Marko Petek Phenodata: None Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_01_TargetSelect

Short Name: 04_prod-qPCR Assay Class: WET Assay Type: qPCR Title: qPCR for quantification of dsRNA production in E coli Description: qPCR for quantification of dsRNA production in E coli pISA Assay creation date: 2021-01-14 pISA Assay creator: Marko Petek Phenodata: None Featuredata: Data:

Short Name: 04_stages-qPCR Assay Class: WET Assay Type: qPCR Title: qPCR of stages samples Description: qPCR of stages samples for target genes pISA Assay creation date: 2021-05-10 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210113.txt Featuredata: Data: Lab manager: Kristina Gruden Assay chemistry: mixed Assay optimisation protocol (file path, link or citation): Pippeting: liquid handling station and manual Reaction volume: 5 ul qPCR platform: HT7900 Fast, ABI (SDS); Viia7, ABI ...

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:

Assay: _A_04_TransRate Short Name: 04_TransRate Assay Class: DRY Assay Type: TransRate Title: TransRate post filtering and reassignment Description: TransRate post filtering and reassignment pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt

Submitter: Maja Zagorscak

Biological problem addressed: Validation

Investigation: _I_STRT

Study: _S_03_stCuSTr

Assay: _A_05_BUSCO Short Name: 05_BUSCO Assay Class: DRY Assay Type: BUSCO Title: BUSCO post filtering and reassignment Description: BUSCO post filtering and reassignment pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt

Submitter: Maja Zagorscak

Biological problem addressed: Validation

Investigation: _I_STRT

Study: _S_03_stCuSTr

Short Name: 05_CPB_gene-annot Assay Class: DRY Assay Type: annot Title: CPB gene annotation using Blast2GO Description: Annotation of CPB predicted genes/proteins using Blast2GO (B2G) suite pISA Assay creation date: 2021-01-14 pISA Assay creator: Marko Petek Phenodata: None 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: 05_extr_reads-rcf Assay Class: DRY Assay Type: rcf Title: Extract reads for specific taxa using recentrifuge (rcf) Description: Extract reads for specific bacterial taxa using recentrifuge for further use in de novo genome assembly pISA Assay creation date: 2021-01-16 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210115.txt Featuredata: Data:

Short Name: 05_MSA_3cvs-GFFmerged Assay Class: DRY Assay Type: GFFmerged Title: MSA 3cv and GFF-merged Description: Multiple sequence alignment of Desiree, PW363, Rywal and ITAG/PGSC pISA Assay creation date: 2020-03-10 pISA Assay creator: Maja Zagorscak Phenodata: None 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:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_SxP10-newG-DE

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:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_SxP1012-finalG

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:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_SxP10-oldG-DE

Short Name: 06_extr_bact-assembly Assay Class: DRY Assay Type: assembly Title: De novo genome assembly of bacteria Description: De novo genome assembly of bacteria from rcf-extracted shotgun metagenomics reads pISA Assay creation date: 2021-01-16 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210115.txt Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_03_Omics

Study: _S_02_metagenome_resp

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: 06_splitter_BLAST-dry Assay Class: DRY Assay Type: dry Title: Split transcripts and BLAST short fragments against insect genomes Description: Split CPB transcripts predicted from the genome into fragments of 21 nt using EMBOSS splitter program and BLASTn againt transcripts of selected insect genomes pISA Assay creation date: 2021-01-14 pISA Assay creator: Marko Petek Phenodata: None Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_01_TargetSelect

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: ...

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_SxP10-newG-DE

Short Name: 06_tr_rep-transrate Assay Class: DRY Assay Type: transrate Title: Cultivar representative transcriptome transrate Description: Transrate on cultivar specific representatives, GFF merged as a reference for CRRB pISA Assay creation date: 2020-03-11 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT

Study: _S_04_stPanTr

Short Name: 07_allReads_meta-assembly Assay Class: DRY Assay Type: assembly Title: De novo assembly of metagenome using metaSPAdes Description: De novo assembly of microbes present in the metagenome using metaSPAdes using all reads without selection but with rigorous filtering and read correction pISA Assay creation date: 2021-01-16 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210115.txt Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_03_Omics

Study: _S_02_metagenome_resp

Short Name: 07_Desiree-mapping Assay Class: DRY Assay Type: mapping Title: Desiree mapping Description: Mapping of Desiree samples (drought stress) to Desiree and Phureja transcriptomes pISA Assay creation date: 2020-03-11 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT

Study: _S_04_stPanTr

Short Name: 07_MergeEvi-dry Assay Class: DRY Assay Type: dry Title: Merge evidence from previous assays for CPB genome Description: Merge all evidence from literature, databases and BLAST results for target gene selection pISA Assay creation date: 2021-01-14 pISA Assay creator: Marko Petek Phenodata: None Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_01_TargetSelect

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:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_SxP10-newG-DE

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:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_SxP10-oldG-DE

Short Name: 08_centrifuge_3cvs-GFFmerged Assay Class: DRY Assay Type: GFFmerged Title: Centrigufe pan-transcriptome sequence classification Description: Classify cv rep transcripts and pan-transcriptome singletons based on taxonomy pISA Assay creation date: 2020-03-11 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT

Study: _S_04_stPanTr

Short Name: 08_SelTargetsA-dry Assay Class: DRY Assay Type: dry Title: Bioinformatics analyses for individual selected target genes Description: In depth bioinformatic analysis for each target gene using various tools to predict possible off-target effects and select a fragment sequence for dsRNA synthesis pISA Assay creation date: 2021-01-14 pISA Assay creator: Marko Petek Phenodata: None Featuredata: Data:

Short Name: 09_annotation-GFFmerged Assay Class: DRY Assay Type: GFFmerged Title: Pan-transcriptome fasta files annotation Description: Annotation of pan-transcriptome and re-annotation of cultivar-specific transcriptomes pISA Assay creation date: 2020-03-11 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:

Empty assay

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: 1 hidden item

Study: FAIRDOMhub API usage in R

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:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

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: 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 ...

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P1_SxPv10vsSxP12

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 ...

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_GAtreat

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: 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 ...

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P1_SxPv10vsSxP12

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). ...

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P1_SPv10T0andT1

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 ...

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P1_SPv10T0andT1

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:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P1_SPv10T2andT3

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 ...

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P1_SPv1TransientExp

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 ...

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P1_SPv10T2andT3

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 ...

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P1_SPv10T2andT3

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, ...

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P1_SxPAltAcTransferases

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:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P1_SxPv10vsSxP12

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 ...

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P1_SxPv12T2

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 ...

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P1_SPv1TransientExp

Files connected to investigation: _I_01_LabTrials

Files connected to investigation: _I_02_FieldTrials

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_02_FieldTrials

Study: Investigation files

Files connected to investigation: _I_03_Omics

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_03_Omics

Study: Investigation files

Files connected to study: _S_01_2019

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_02_FieldTrials

Study: _S_01_2019

Files connected to study: _S_01_ns-dsRNA_trans

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_03_Omics

Study: _S_01_ns-dsRNA_trans

Files connected to study: _S_01_TargetSelect

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_01_TargetSelect

Files connected to study: _S_02_2020

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_02_FieldTrials

Study: _S_02_2020

Files connected to study: _S_02_dsRNAorder

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_02_dsRNAorder

Files connected to study: _S_02_metagenome_resp

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_03_Omics

Study: _S_02_metagenome_resp

Files connected to study: _S_03_dsRNAprod

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_03_dsRNAprod

Files connected to study: _S_04_Stages

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_04_Stages

Files connected to study: _S_05_jun2016

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_05_jun2016

Files connected to study: _S_06_oct2016

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_06_oct2016

Files connected to study: _S_07_dec2016

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_07_dec2016

Files connected to study: _S_08_jan2017

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_08_jan2017

Files connected to study: _S_09_jun2017

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_09_jun2017

Files connected to study: _S_10_apr2018

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_10_apr2018

Files connected to study: _S_11_may2018

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_01_LabTrials

Study: _S_11_may2018

Files connected to study: _S_P1_SPv10T0andT1

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P1_SPv10T0andT1

Files connected to study: _S_P1_SPv10T2andT3

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P1_SPv10T2andT3

Files connected to study: _S_P1_SPv1TransientExp

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P1_SPv1TransientExp

Files connected to study: _S_P1_SxPAltAcTransferases

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P1_SxPAltAcTransferases

Files connected to study: _S_P1_SxPv10vsSxP12

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P1_SxPv10vsSxP12

Files connected to study: _S_P1_SxPv12T2

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P1_SxPv12T2

Files connected to study: _S_P4_CoExpNetViz

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_CoExpNetViz

Files connected to study: _S_P4_DiNAR

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_DiNAR

Files connected to study: _S_P4_GAtreat

Files connected to study: _S_P4_SxP10-newG-DE

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_SxP10-newG-DE

Files connected to study: _S_P4_SxP10-oldG-DE

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_SxP10-oldG-DE

Files connected to study: _S_P4_SxP1012-finalG

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_SxP1012-finalG

Files connected to study: _S_P4_SxP12-newG-DE

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_SxP12-newG-DE

  • Comparison of metabolic flux distribution in carbon core metabolism (EMP, PPP, TCA) of Bacillus subtilis under 3 different conditions: "salt-free" reference, "stress" chemostat, "osmoprotected" chemostat.
  • Model created using OpenFLUX and Microsoft Excel
  • Model computed using MatLAB

2D Gels in wild type and mutants grown or incubated under several conditions: starvation, potassium limiting or different growth phases.

Is it possible to see changes in the proteome after starvation in 2D- Gels? Preparation of 2D Gels of cells incubated different periods of time in the absence of potassium.

No description specified

"3PG is an acronym for Physiological Principles Predicting Growth. It is a generalized forest carbon allocation model, published by Landsberg and Waring (1997), that works with any forest biome and can be run as an Excel spreadsheet by practicing foresters given a few days of training. The model uses relatively simple and readily available inputs such as species growth tables, latitude, aspect, weather records, edaphic variables, stand age, and stand density to derive monthly estimates of gross ...

Submitter: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Investigation: Muetzelfeldt, Robert

Study: 3PG - PLM_12

Contains the analysis of the internal metabolite concentrations of the 40 independend samples Pearson correlation was used to generate heatmaps Pearson correlation with p-value cutof of 0.001 was used and as input for a correlation network (grouping using H-clust) Principal component analysis was performed on samples, F-ion and H-ion data combined and seperately Zip files contains the data (FC.txt), PCA and heatmap plots and the script to re-generate these plots

Submitter: Niels Zondervan

Biological problem addressed: Model Analysis Type

Investigation: Modelling of M. pneumoniae metabolism

Study: Metabolomics measurements

Simulation of OE mutants targetting enzymes in the model, combined with metabolite concentrations and enzyme fold change of from the 40 samples. For each second mutant the enzyme concentrations in case of OE and KO mutants in updated and the metabolite concentrations of the second sample are loaded in the model. Using this approach the model approximately predicts combinatorial effects of OE mutations with other mutations, perturbations and time series concentrations.

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