Assays

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832 Assays visible to you, out of a total of 1679

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

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:

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_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: __

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_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: 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:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_SxP10-oldG-DE

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:

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_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

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

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: 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: 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:

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_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: 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

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

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: 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: 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

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: 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

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