Assays

What is an Assay?
978 Assays visible to you, out of a total of 1941
No description specified

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

Study: Microbial-induced calcium carbonate precipitati...

In vitro reconstitution of the PGK, GAPHD, TPI and FBPAase enzymes from S. solfataricus

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) ...

correlations of starch mobilisation and fresh weight under single parameter changes

No description specified

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 ...

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

Study: Simulation Foundry for Methanol-Water Mixtures

Data derived from RNAseq

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

Study: In vivo II - GW and WY: Effects on cod lipid me...

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 ...

No description specified

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 ...

No description specified

Submitter: Fekadu Yadetie

Assay type: RNA-seq

Technology type: Next generation sequencing

Investigation: 1 hidden item

Study: Effects of BaP and EE2 treatments on transcript...

RNAseq data for L.ferriphilum samples

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 ...

No description specified

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.

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).

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.

No description specified

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.

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