Assays
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).
Submitter: Marta Eide
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: 1 hidden item
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
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