Assays
What is an Assay?Filters
Biomass, leaf number and metabolites in Col0 (WT), prr7, prr7prr9, and lsf1. Metabolite data from plants after 28 days of growth were analysed most (27 days 'end of night', 28 days 'end of day' and 'end of night'). The data file also includes data from 21 days of growth ('end of day' and 'end of night'), which is useful for comparison to early-flowering plants not tested here, such as the lhycca1 double mutant, that flower before 28 days, altering their physiology.
Submitter: Daniel Seaton
Assay type: Organism or Strain Characteristics
Technology type: Technology Type
Investigation: Prediction and analysis of phenotypes in the Ar...
Submitter: Daniel Seaton
Biological problem addressed: Model Analysis Type
Investigation: Prediction and analysis of phenotypes in the Ar...
The data is submitted to the PRIDE repository, and will be linked here.
Submitter: Marta Eide
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: 1 hidden item
Targeted lipidomic analysis was performed on plasma and isolated liver microsomes of eight male fish from solvent control (Control) and High-Dose groups (n = 8) at Cinta Porte’s lab at CSIC, Spain, using Flow Injection Analysis High-Resolution Mass Spectrometry (FIA-HRMS).
The data is submitted to the MetaboLights repository.
Submitter: Marta Eide
Assay type: Metabolomics
Technology type: Mass Spectrometry
Investigation: 1 hidden item
This Jupyter Notebook assists you in understanding how a Selwyn Test works.
For help on installing the classical Jupyter Notebook, see here: https://jupyter.org/install
For documentation about Juypter Notebooks, see here: https://jupyter-notebook.readthedocs.io/en/stable/
There are multiple tutorials online that help you to learn how to use a Jupyter notebook.
The notebook is provided as an .ipynb and as a .pdf file.
The plots the script generates with the default values are also given as .png ...
Submitter: Gudrun Gygli
Biological problem addressed: Model Analysis Type
Investigation: On the reproducibility of enzyme reactions and ...
Study: Selwyn Test
This Jupyter Notebook assists you in understanding how a progress curve experiment can look like.
For help on installing the classical Jupyter Notebook, see here: https://jupyter.org/install
For documentation about Juypter Notebooks, see here: https://jupyter-notebook.readthedocs.io/en/stable/
There are multiple tutorials online that help you to learn how to use a Jupyter notebook.
The notebook is provided as an .ipynb and as a .pdf file.
The plots the script generates with the default values are ...
Submitter: Gudrun Gygli
Biological problem addressed: Model Analysis Type
Investigation: On the reproducibility of enzyme reactions and ...
Study: Progress Curve Analysis
This Jupyter Notebook assists you in the analysis of initial rate experiments.
For help on installing the classical Jupyter Notebook, see here: https://jupyter.org/install
For documentation about Juypter Notebooks, see here: https://jupyter-notebook.readthedocs.io/en/stable/
There are multiple tutorials online that help you to learn how to use a Jupyter notebook.
The notebook is provided as an .ipynb and as a .pdf file. The plots the script generates with the default input data are also given as ...
Submitter: Gudrun Gygli
Biological problem addressed: Model Analysis Type
Investigation: On the reproducibility of enzyme reactions and ...
Submitter: Dikshant Pradhan
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: MIT SRP
Submitter: Dikshant Pradhan
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: MIT SRP
Submitter: Dikshant Pradhan
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: MIT SRP
Submitter: Dikshant Pradhan
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: MIT SRP
Submitter: Dikshant Pradhan
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: MIT SRP
Submitter: Dikshant Pradhan
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: MIT SRP
Submitter: Dikshant Pradhan
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: MIT SRP
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: 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:
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_03_Omics
Study: _S_02_metagenome_resp
Short Name: 03-Centrifuge Assay Class: DRY Assay Type: Centrifuge Title: Centrifuge classification of DNA reads Description: Taxonomic classification of shotgun gDNA Illumina reads from CPB gut microbiome and visualization using pavian pISA Assay creation date: 2021-01-15 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210115.txt Featuredata: Data: http://stork/dirindex/fitostorage/fitostorageA/datarepo/ngs_omics/NGS_lde_dna-seq_2018_mpe_CPB-gut-metagenome/data/
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_03_Omics
Study: _S_02_metagenome_resp
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
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:
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_03_Omics
Study: _S_02_metagenome_resp
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: 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:
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_03_Omics
Study: _S_02_metagenome_resp
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:
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_03_Omics
Study: _S_01_ns-dsRNA_trans
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
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_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 investigation: _I_03_Omics
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_03_Omics
Study: Investigation files
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_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
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_01_2019
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_02_FieldTrials
Study: _S_01_2019