Assays

430 Assays visible to you, out of a total of 755

Total lipids are extracted from tissues of white muscle, liver and whole brain from three fish per dietary treatment.

Contributor: Sahar Hassani

Assay type: Experimental Assay Type

Technology type: Technology Type

Snapshots: No snapshots

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.

Contributor: Sahar Hassani

Assay type: Experimental Assay Type

Technology type: Technology Type

Snapshots: No snapshots

The three different CRISPR target sites within the elovl2 gene (T1-3) were characterised by Sanger sequencing, sequencing on average 8 clones per individual.

Contributor: Sahar Hassani

Assay type: Experimental Assay Type

Technology type: Technology Type

Snapshots: No snapshots

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Contributor: Ziva Ramsak

Assay type: Metabolite Profiling

Technology type: Gas Chromatography Mass Spectrometry

Snapshots: No snapshots

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Contributor: Ziva Ramsak

Assay type: Protein Expression Profiling

Technology type: Orbitrap Velos

Snapshots: No snapshots

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Contributor: Ziva Ramsak

Assay type: Q_PCR

Technology type: qPCR

Snapshots: No snapshots

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Contributor: Ziva Ramsak

Assay type: MicroRNA Profiling

Technology type: Next generation sequencing

Snapshots: No snapshots

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Contributor: Ziva Ramsak

Assay type: Degradome-Seq

Technology type: Next generation sequencing

Snapshots: No snapshots

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Contributor: Ziva Ramsak

Assay type: Q_PCR

Technology type: qPCR

Snapshots: No snapshots

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Contributor: Ziva Ramsak

Assay type: Gene Expression Profiling

Technology type: Custom Array

Snapshots: No snapshots

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Contributor: Ziva Ramsak

Assay type: Q_PCR

Technology type: qPCR

Snapshots: No snapshots

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Contributor: Ziva Ramsak

Assay type: Phenotype observation

Technology type: Leaf Chamber Fluorometer

Snapshots: No snapshots

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Contributor: Ziva Ramsak

Assay type: Phenotype observation

Technology type: Imaging

Snapshots: No snapshots

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
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Contributor: Sahar Hassani

Assay type: Experimental Assay Type

Technology type: Technology Type

Snapshots: No snapshots

The models in this record were published in Flis et al. Royal Society Open Biology 2015. They will be submitted to Biomodels when we have a PubMed ID for the paper.

Original model: Arabidopsis clock model P2011.1.1 from Pokhilko et al. Mol Syst. Biol. 2012, http://dx.doi.org/10.1038/msb.2012.6

Photothermal model for Arabidopsis development, as published, converted to Simile format by Yin-Hoon Chew. Note that the XML file is just a dummy SBML file, the .SML is the working model file. Simile can read csv files (as attached) for meteorological data (hourly temperature, sunrise, sunset). Users only need to change the directory of the input variables. I have also attached the set of parameter values for each genotype.

Related Publications
Wilczek et al.
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Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

Photothermal model for Arabidopsis development, as published, converted to Simile format by Yin-Hoon Chew. Note that the XML file is just a dummy SBML file, the .SML is the working model file. Simile can read csv files (as attached) for meteorological data (hourly temperature, sunrise, sunset). Users only need to change the directory of the input variables. I have also attached the set of parameter values for each genotype.

Related Publications
Wilczek et al.
...

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

Detailed model of starch metabolism from Sorokina et al. BMC Sys Bio 2011. First upload is a draft.

Related Publications
Sorokina et al (2011). BMicroarray data can predict diurnal changes of starch content in the picoalga Ostreococcus.. BMC Systems Biology. Retrieved from: http://www.ncbi.nlm.nih.gov/pubmed/21352558

Originally submitted to PLaSMo on 2011-08-12 15:34:00

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

The model shows how the CONSTANS gene and protein in Arabidopsis thaliana forms a day-length sensor. It corresponds to Model 3 in the publication of Salazar et al. 2009. Matlab versions of all the models in the paper are attached to this record as a ZIP archive, as are all the data waveforms curated from the literature to constrain the model. Further information may be available via links from the authors web site (www.amillar.org). Simulation
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Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

The model shows how the CONSTANS gene and protein in Arabidopsis thaliana forms a day-length sensor. It corresponds to Model 3 in the publication of Salazar et al. 2009. Matlab versions of all the models in the paper are attached to this record as a ZIP archive, as are all the data waveforms curated from the literature to constrain the model. Further information may be available via links from the authors web site (www.amillar.org). Simulation
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Andrew's work-in-progress P2012 version. NB KNOWN PROBLEMS do not use lightly. Derived from PLM_49, after removing ABA regulation and tidying up the SBML in COPASI. Please see version comments for IMPORTANT notes.

Comments


No parameters constrained in version 1 file.


2013-02-26 17:31:26 3 amillar2 andrew.millar@ed.ac.uk


Compiled successfully in SBSI for optimisation.


2013-02-26 17:28:18 3 amillar2 andrew.millar@ed.ac.uk

Version
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Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

Andrew's work-in-progress P2012 version. NB KNOWN PROBLEMS do not use lightly. Derived from PLM_49, after removing ABA regulation and tidying up the SBML in COPASI. Please see version comments for IMPORTANT notes.

Comments


No parameters constrained in version 1 file.


2013-02-26 17:31:26 3 amillar2 andrew.millar@ed.ac.uk


Compiled successfully in SBSI for optimisation.


2013-02-26 17:28:18 3 amillar2 andrew.millar@ed.ac.uk

Version
...

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

Draft of MEP pathway for isoprenoid synthesis, created 2012-2013 by Oender Kartal in the Gruissem lab. He notes "It contains some annotations and references for the parameter values and rate equations and produces a stable steady state, so you can do some control analysis. It simulates day-metabolism, since the MEP Pathway is supposedly active during the day." Unpublished, for use by TiMet consortium only.

Originally submitted to PLaSMo on 2013-09-13 09:10:53

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

This is a version derived from a model from the article: Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana. Locke JC, Kozma-Bognár L, Gould PD, Fehér B, Kevei E, Nagy F, Turner MS, Hall A, Millar AJ Mol. Syst. Biol.2006;Volume:2;Page:59 17102804,   The model describes a three loop circuit of the Arabidopsis circadian clock. It provides initial conditions,
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Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

This version is derived from a model from the article: Extension of a genetic network model by iterative experimentation and mathematical analysis. Locke JC, Southern MM, Kozma-Bognár L, Hibberd V, Brown PE, Turner MS, Millar AJ Mol. Syst. Biol. 2005; 1: 2005.0013 16729048,  SBML model of the interlocked feedback loop network The model describes the circuit depicted in Fig. 4 and reproduces the simulations
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Temperature-sensitive version of Pokhilko 2010 Arabidopsis clock model, from Biomodels BIOMD00273, prepared by Mirela Domijan for the Gould et al. paper on cryptochrome influences on circadian rhythms.    Molecular Systems Biology 9 Article number: 650  doi:10.1038/msb.2013.7 Published online: 19 March 2013 Citation: Molecular Systems Biology 9:650 Network balance via CRY signalling controls the Arabidopsis circadian clock over ambient temperatures Gould,
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Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

Temperature-sensitive version of Pokhilko 2010 Arabidopsis clock model, from Biomodels BIOMD00273, prepared by Mirela Domijan for the Gould et al. paper on cryptochrome influences on circadian rhythms.    Molecular Systems Biology 9 Article number: 650  doi:10.1038/msb.2013.7 Published online: 19 March 2013 Citation: Molecular Systems Biology 9:650 Network balance via CRY signalling controls the Arabidopsis circadian clock over ambient temperatures Gould,
...

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

A cell-level model of the Arabidopsis root elongation zone. This spatial model is divided up into biological cells which are further divided into simulation boxes. The original model was designed to investigate how canal cells can accumulate auxin over time rather than to investigate the transport of auxin through the canal cells per se. The main outputs of the simulations in the original paper were the steady state ratios of auxin in the canal cell protoplasts to that in the parenchyma cell
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A cell-level model of the Arabidopsis root elongation zone. This spatial model is divided up into biological cells which are further divided into simulation boxes. The original model was designed to investigate how canal cells can accumulate auxin over time rather than to investigate the transport of auxin through the canal cells per se. The main outputs of the simulations in the original paper were the steady state ratios of auxin in the canal cell protoplasts to that in the parenchyma cell
...

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

Andrew's "ongoing work" record for the P2011 clock model. Many different versions, with annotations made during SBSI development in 2011-2013 - see version records.

Version Comments


Corrected m1 parameter and range, tested in SBSI




Originally submitted to PLaSMo on 2012-05-31 22:18:27

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

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