Assays
What is an Assay?Filters
Submitter: Dikshant Pradhan
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: MIT SRP
Data for Raman spectroscopy shown in publication: Microbial-induced calcium carbonate precipitation: An experimental toolbox for in situ and real-time investigation of micro-scale pH evolution.
Included are the Raman data for precipitation after 1 minute recton time, 3 minutes reaction time and 15 minutes reaction time.
Submitter: Jennifer Zehner
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: 1 hidden item
In vitro reconstitution of the PGK, GAPHD, TPI and FBPAase enzymes from S. solfataricus
Submitter: Jacky Snoep
Biological problem addressed: Metabolic Network
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Study: Model Gluconeogenesis
Despite high similarity in sequence and catalytic properties, the L-lactate dehydrogenases (LDH) in lactic acid bacteria (LAB) display differences in their regulation which may arise from their adaptation to different habitats. We combined experimental and computational approaches to investigate the effects of fructose-1,6-bisphosphate (FBP), phosphate (Pi) and ionic strength (NaCl concentration) on 6 LDHs from 4 LABs studied at pH 6 and pH 7. We find: (1) The extent of activation by FBP (Kact) ...
Submitter: Anna Feldman-Salit
Biological problem addressed: Metabolism
Investigation: Investigation of glycolysis and pyruvate branch...
correlations of starch mobilisation and fresh weight under single parameter changes
Submitter: Andrew Millar
Biological problem addressed: Model Analysis Type
Investigation: Prediction and analysis of phenotypes in the Ar...
Submitter: Sandra Maass
Assay type: Protein Expression Profiling
Technology type: Mass Spectrometry
Investigation: The transition from growing to non-growing Baci...
Submitter: Sandra Maass
Assay type: Protein Expression Profiling
Technology type: Mass Spectrometry
Investigation: Multiomics study of Bacillus subtilis under osm...
This section contains the links to the tools used for reproducing the computational results presented in U2019. This is required because SloppyCell is under the risk of becoming rotting code. Using Docker we can assure some persistence for the computational environment that allows to run SloppyCell.
The associated git repository can be found in https://github.com/jurquiza/Urquiza2019a.git which can be cloned.
The docker image can either be pulled from the docker hub site
docker pull ...
Submitter: Uriel Urquiza Garcia
Biological problem addressed: Model Analysis Type
Investigation: Absolute units in Arabidopsis clock models up t...
Here would be the results from the Analysis part of the Simulation foundry. For the newest version, which was improved based on reviewers comments to represent best practices, of the Simulation Foundry for Methanol-Water mixtures no such results exist yet.
Submitter: Gudrun Gygli
Biological problem addressed: various analyses of molecular dynamics simulations
Investigation: 1 hidden item
Docking results of pteridine-based compounds in different target PTR1 and DHFR receptors and the off-target human DHFR when treating ligands as flexible and the protein receptors as a rigid-body.
Submitter: Ina Poehner
Biological problem addressed: Model Analysis Type
Investigation: Pteridines as anti-kinetoplastid folate-pathway...
Data derived from RNAseq
Submitter: Malte Herold
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Reverse Engineering Directed Gene Regulatory Ne...
Study: Supplementary files
Liver samples from Atlantic cod males. Total RNA isolated using TRI Reagent (Fekadu Yadetie). Sequencing performed with Illumina Stranded mRNA (sequencing poly-A mRNA) at Genomic Core Facility at UiB/Haukeland (contact person Rita Holdhus).
The data sets are submitted to the ArrayExpress repository, and will be linked here.
Submitter: Marta Eide
Assay type: Transcriptomics
Technology type: Rna-seq
Investigation: 1 hidden item
From the "data accessibility" section of Life-stage associated remodeling of lipid metabolism regulation in Atlantic salmon. (Publication):
Supplementary files have been deposited to datadryad.org under the accession: https://doi.org/10.5061/dryad.j4h65. Raw RNA-Seq data have been deposited into European Nucleotide Archive (ENA) under the project Accession no. PRJEB24480.
Dead links 2022-06-29 (the Shiny ...
Submitter: Graceline Tina Kirubakaran
Assay type: RNA-seq
Technology type: Next generation sequencing
Investigation: Omega-3 metabolism of salmon in relation to die...
Submitter: Jacqueline Wolf
Assay type: RNA-seq Profiling
Technology type: Rna-seq
Investigation: Amino acid degradation in Sulfolobus solfataric...
Submitter: Jacqueline Wolf
Assay type: Experimental Assay Type
Technology type: Rna-seq
Investigation: Phenol degradation in Saccharolobus solfataricu...
Submitter: Theresa Kouril
Assay type: RNA-seq Profiling
Technology type: Next generation sequencing
Investigation: L-fucose degradation in Sulfolobus solfataricus P2
S.pneumoniae D39 cells (wild type and delta greA) were grown in C+Y medium and cells were harvested for total RNA isolation at mid-exponential growth (OD600nm 0.3 for wt, 0.25 for delta greA). Total RNA was isolated as described before (Kloosterman et al 2006). The total RNA samples were examined by capillary electrophoresis. dephosphorylated with antarctic phosphatase followed by treatment with polynucleotide kinase (PNK). Afterwards, samples were poly(A)-tailed using poly(A) polymerase. Then a ...
Submitter: Jan-Willem Veening
Assay type: Transcriptomics
Technology type: Technology Type
Investigation: Wetlab approach to transcription fidelity
Submitter: Fekadu Yadetie
Assay type: RNA-seq
Technology type: Next generation sequencing
Investigation: 1 hidden item
RNAseq data for L.ferriphilum samples
Submitter: Malte Herold
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Multi -omics reveal lifestyle of acidophile, mi...
Study: Omics_data_analysis
Stranded RNAseq libraries were prepared from 1µg total RNA from liver tissue using TruSeq Stranded mRNA library preparation kit (Illumina, San Diego, USA) using double unique indices (#20022371), according to the manufacturer's instruction (Part 15031057 Rev.E). Libraries were sequenced at the Norwegian Sequencing Centre (NSC). All libraries were pooled, and the same pool was sequenced on 4 flow cell lanes on a HiSeq 3000 machine (Illumina), generating 100bp single-end reads. RNA sequencing files ...
Submitter: Sahar Hassani
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Knockout omega-3 genes to perturb LC-PUFA metab...
Study: ELOVL2 Knockout
Rawdata for RNAseq derived from biofilms on chalcopyrite grains
Submitter: Malte Herold
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: SysMetEx - Dataset collection
Link to RNAseq raw data
Submitter: Malte Herold
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: SysMetEx - Dataset collection
Study: Planktonic cells
RNAseq raw data derived from continuous culture samples
Submitter: Malte Herold
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: SysMetEx - Dataset collection
Study: Continuous cultures
Submitter: Yang Jin
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Knockout omega-3 genes to perturb LC-PUFA metab...
Study: FADS Knockout
RNAseq is utilised to validate the SnpEff annotation predictions for aberrant splicing. For this purpose the percentage exon retention for exons 4, 6 and 7 are calculated using RNAseq data.
Submitter: Sahar Hassani
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Knockout omega-3 genes to perturb LC-PUFA metab...
Study: ELOVL2 Knockout
RobOKoD algorithm was, designed then implemented as part of a study in RobOKoD: microbial strain design for (over)production of target compounds. (http://fairdomhub.org/publications/236). It was used to generate a strain of e.coli for producing butanol, that was then compared to an experimental strain. It was shown to perform better than similar methods (OptKnock, and RobustKnock).
Submitter: Natalie Stanford
Biological problem addressed: Model Analysis Type
Investigation: Designing a new way to predict engineering stra...
RobustKnock algorithm was used as part of a study in RobOKoD: microbial strain design for (over)production of target compounds. (http://fairdomhub.org/publications/236). It was used to generate a strain of e.coli for producing butanol, that was then compared to an experimental strain.
Submitter: Natalie Stanford
Biological problem addressed: Model Analysis Type
Investigation: Designing a new way to predict engineering stra...
Submitter: Falko Krause
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: K+ Starvation in Saccharomyces cerevisiae
Study: Transcriptional Profile
A example of an RT-PCR Excel template. RT-PCR is Reverse Transcriptase PCR (NOT to be confused with Real Time PCR, which is normally referred to as qPCR)
This template was taken from the GEO website (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html) and modified to conform to the SysMO-JERM (Just enough Results Model) for transcriptomics. Using templates will mean easier submission to public databases on publication and greater consistency of data in SEEK.
Submitter: Katy Wolstencroft
Assay type: Gene Expression Profiling
Technology type: qRT-PCR
Investigation: Creating data sheet template for 'omics data