Assays

23 Assays visible to you, out of a total of 61

PoLiMeR - Polymers in the Liver: Metabolism and Regulation

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The behaviour of a published MCAD-KO HepG2 cell line was compared to that of a wild-type HepG2 cell line in terms of the changes in acyl-CoA and acylcarnitine levels (measured by HILIC-MS/MS) and gene expression pertaining to CoA metabolism (characterised by qPCR). Additionally, the incorporation of label from stable isotope-labelled pantothenate (vitamine B5) was over 24 hours of exposure to an energetic stressor was also investigated.

Submitter: Christoff Odendaal

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Mitochondrial fatty acid oxidation in human liver

Study: Sequestration of CoA and adaptation of CoA meta...

Organisms: Homo sapiens (batch)

SOPs: No SOPs

Data files: HepG2 CoA labelling data, palmitate/no-glucose ..., HepG2 acyl-CoA measurements, palmitate/low-gluc..., HepG2 acyl-CoA measurements, palmitate/no-gluco..., HepG2 acyl-CoA/acylcarnitine measurements stati..., HepG2 acyl-CoA/acylcarnitine measurements stati..., HepG2 acylcarnitine measurements, palmitate/low..., HepG2 acylcarnitine measurements, palmitate/no-..., HepG2 qPCR statistical significance, palmitate/..., HepG2 qPCR statistical significance, palmitate/..., HepG2 qPCR, palmitate/low-glucose (Fig. S11), HepG2 qPCR, palmitate/no-glucose (Fig. S9)

Snapshots: No snapshots

Created: 9th May 2025 at 14:50, Last updated: 16th May 2025 at 11:45

Model analysis for HSD11B1/AKR1C3 ratio experiment

Steroid biosynthesis

Model simulations for 24h incubations with different ratios of HSD11B1 andd AKR1C3 transfected HEK293 cells are given in Mathematica notebook format.

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Effect of 11BHSD inhibition on 11-ketotestoster...

Study: HSD11B1/AKR1C3 ratio experiments

Organisms: Homo sapiens

Models: Model simulation of metabolite profiles after 2...

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 16th Feb 2024 at 13:49, Last updated: 17th Mar 2024 at 08:52

Data for HSD11B1/AKR1C3 ratio experiment in Fig. 2

Steroid biosynthesis

Excel file with metablite profiles after 24 h incubation with different ratios of 11HSDB1 and AKR1C3.

Submitter: Jacky Snoep

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Effect of 11BHSD inhibition on 11-ketotestoster...

Study: HSD11B1/AKR1C3 ratio experiments

Organisms: Homo sapiens

SOPs: No SOPs

Data files: Ratio experiments

Snapshots: No snapshots

Created: 16th Feb 2024 at 13:30, Last updated: 17th Mar 2024 at 08:50

GAPDH and flux inhibition in MCF7 and MDA231cells

Glucose metabolism in cancer cell lines

No description specified

Submitter: Theresa Kouril

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Metabolic control analysis of glyceraldehyde 3-...

Study: Iodoacetic acid (IAA) titrations in cancer cell...

Organisms: Homo sapiens

SOPs: SOP_Cancer cell lines_standard cell culture, SOP_Inhibitor titration intact cells, SOP_Preparation of cell lysates, SOP_Quantification of glycolytic flux (glucose,...

Data files: MCF7_IAA titration_flux_GAPDH_intact cells, MDA231_IAA titration_flux_GAPDH_intact cells

Snapshots: No snapshots

Created: 12th Jul 2023 at 13:18, Last updated: 19th Jul 2023 at 10:19

HepG2 oxygen consumption

PoLiMeR - Polymers in the Liver: Metabolism and Regulation

(Show All)

Validation of model's ability to predict oxygen consumption flux as measured usign permeabilised cells in an Oroboros Oxygraph. Generates Fig. 2A in the associated publication.

Download "Model_notebooks.rar", unzip, and run: "2, generate-model-Oroboros-validation-[needs(1)]-20221109.nb" and "4, Fig2A-Oroboros-simulation-data-[needs-(1-2-and-3)]-20221109.nb" after running "1, generate-model-20221109.nb"

Submitter: Christoff Odendaal

Biological problem addressed: Validation

Investigation: Mitochondrial fatty acid oxidation in human liver

Study: Model validation

Organisms: Homo sapiens

Models: Model notebooks, odendaal2

SOPs: No SOPs

Data files: HepG2 protein concentration for O2 consumption ..., Oxygen concentration and consumption flux in pe...

Snapshots: No snapshots

Created: 23rd Feb 2023 at 14:41, Last updated: 12th Jun 2023 at 13:30

Standard-based Excel template for metabolomics data

SysMO DB, FAIRDOM, FAIRDOM user meeting

Dear SEEK users, this Assay is just an example Excel sheet for intracellular metabolites concentration measurements performed using cell culture growing in chemostat

Submitter: Olga Krebs

Assay type: Metabolite Profiling

Technology type: Mass Spectrometry

Investigation: Creating data sheet template for 'omics data

Study: Creating template for metabolomics data

Organisms: Saccharomyces cerevisiae, Homo sapiens : MCF-7 (wild-type / wild-type)

SOPs: No SOPs

Data files: Excel sheet template : concentrations of intrac..., The FAIR Guiding Principles for scientific data...

Snapshots: No snapshots

Created: 10th Jun 2009 at 17:22, Last updated: 30th Jun 2022 at 08:43

Multiscale simulation using PhysiBoSS with the perturbed models identified by MaBoSS

COVID-19 Disease Map

No description specified

Submitter: Arnau Montagud

Biological problem addressed: Gene Regulatory Network

Investigation: PhysiBoSS-COVID: the Boolean modelling of COVID...

Study: Exploring genetic perturbations that maximise a...

Organisms: Homo sapiens

Models: No Models

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 13th Aug 2021 at 08:01

Use of MaBoSS to find genetic perturbations that maximise apopotosis phenotype in a Boolean model

COVID-19 Disease Map

No description specified

Submitter: Arnau Montagud

Biological problem addressed: Gene Regulatory Network

Investigation: PhysiBoSS-COVID: the Boolean modelling of COVID...

Study: Exploring genetic perturbations that maximise a...

Organisms: Homo sapiens

Models: No Models

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 13th Aug 2021 at 08:00

Comprehensive model of ROS management

Service to Milano-Bicocca with respect to their ATP-ROS model (Active NOW), Make Me My Model, Service to LCSB (Luxembourg) with respect to ROS management in Parkinson’s disease and cancer model (Active NOW), ROS detailed model for MSB manucript

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No description specified

Submitter: Alexey Kolodkin

Biological problem addressed: Model Analysis Type

Investigation: ROS networks: designs, aging, Parkinson's disea...

Study: ROS Models and Data for NPJ Systems Biology and...

Organisms: Homo sapiens

Models: Calibrated comprehensive model of ROS management, Calibrated comprehensive model of ROS managemen..., Detailed model of ROS management

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 10th Jul 2020 at 18:17, Last updated: 12th Jul 2020 at 19:01

Digitized pharmacokinetics data (Spigset1999a)

Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF)

Data digitized from publication.

Spigset1999a Description

Submitter: Matthias König

Assay type:

Technology type:

Investigation: MM-PLF: Multiscale modeling for personalized li...

Study: PKDB Caffeine Study

Organisms: Homo sapiens

SOPs: No SOPs

Data files: CSV (Spigset1999a), PNG (Spigset1999a)

Snapshots: No snapshots

Created: 19th Jul 2019 at 13:58, Last updated: 19th Jul 2019 at 14:00

Digitized pharmacokinetics data (Jeppesen1996)

Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF)

Data digitized from publication.

Jeppesen1996 Description

Submitter: Matthias König

Assay type:

Technology type:

Investigation: MM-PLF: Multiscale modeling for personalized li...

Study: PKDB Caffeine Study

Organisms: Homo sapiens

SOPs: No SOPs

Data files: CSV (Jeppesen1996), PNG (Jeppesen1996)

Snapshots: No snapshots

Created: 19th Jul 2019 at 13:57, Last updated: 19th Jul 2019 at 14:00

Digitized pharmacokinetics data (Oh2012)

Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF)

Data digitized from publication.

Oh2012 Description

Submitter: Matthias König

Assay type:

Technology type:

Investigation: MM-PLF: Multiscale modeling for personalized li...

Study: PKDB Caffeine Study

Organisms: Homo sapiens

SOPs: No SOPs

Data files: CSV (Oh2012), PNG (Oh2012)

Snapshots: No snapshots

Created: 19th Jul 2019 at 13:57, Last updated: 19th Jul 2019 at 14:00

Digitized pharmacokinetics data (Healy1991)

Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF)

Data digitized from publication.

Healy1991 Description

Submitter: Matthias König

Assay type:

Technology type:

Investigation: MM-PLF: Multiscale modeling for personalized li...

Study: PKDB Caffeine Study

Organisms: Homo sapiens

SOPs: No SOPs

Data files: CSV (Healy1991), PNG (Healy1991)

Snapshots: No snapshots

Created: 19th Jul 2019 at 13:57, Last updated: 19th Jul 2019 at 14:00

Digitized pharmacokinetics data (Akinyinka2000)

Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF)

Data digitized from publication.

Akinyinka2000 Description

Submitter: Matthias König

Assay type:

Technology type:

Investigation: MM-PLF: Multiscale modeling for personalized li...

Study: PKDB Caffeine Study

Organisms: Homo sapiens

SOPs: No SOPs

Data files: CSV (Akinyinka2000), PNG (Akinyinka2000)

Snapshots: No snapshots

Created: 19th Jul 2019 at 13:57, Last updated: 19th Jul 2019 at 14:00

Digitized pharmacokinetics data (Kakuda2014)

Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF)

Data digitized from publication.

Kakuda2014 Description

Submitter: Matthias König

Assay type:

Technology type:

Investigation: MM-PLF: Multiscale modeling for personalized li...

Study: PKDB Caffeine Study

Organisms: Homo sapiens

SOPs: No SOPs

Data files: CSV (Kakuda2014), PNG (Kakuda2014)

Snapshots: No snapshots

Created: 19th Jul 2019 at 13:57, Last updated: 19th Jul 2019 at 14:00

Digitized pharmacokinetics data (Haller2002)

Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF)

Data digitized from publication.

Haller2002 Description

Submitter: Matthias König

Assay type:

Technology type:

Investigation: MM-PLF: Multiscale modeling for personalized li...

Study: PKDB Caffeine Study

Organisms: Homo sapiens

SOPs: No SOPs

Data files: CSV (Haller2002), PNG (Haller2002)

Snapshots: No snapshots

Created: 19th Jul 2019 at 13:57, Last updated: 19th Jul 2019 at 14:00

Digitized pharmacokinetics data (Amchin1999)

Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF)

Data digitized from publication.

Amchin1999 Description

Submitter: Matthias König

Assay type:

Technology type:

Investigation: MM-PLF: Multiscale modeling for personalized li...

Study: PKDB Caffeine Study

Organisms: Homo sapiens

SOPs: No SOPs

Data files: CSV (Amchin1999), PNG (Amchin1999)

Snapshots: No snapshots

Created: 19th Jul 2019 at 13:57, Last updated: 19th Jul 2019 at 13:59

Digitized pharmacokinetics data (Kaplan1997)

Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF)

Data digitized from publication.

Kaplan1997 Description

Submitter: Matthias König

Assay type:

Technology type:

Investigation: MM-PLF: Multiscale modeling for personalized li...

Study: PKDB Caffeine Study

Organisms: Homo sapiens

SOPs: No SOPs

Data files: CSV (Kaplan1997), PNG (Kaplan1997)

Snapshots: No snapshots

Created: 19th Jul 2019 at 13:57, Last updated: 19th Jul 2019 at 13:59

Digitized pharmacokinetics data (Blanchard1983a)

Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF)

Data digitized from publication.

Blanchard1983a Description

Submitter: Matthias König

Assay type:

Technology type:

Investigation: MM-PLF: Multiscale modeling for personalized li...

Study: PKDB Caffeine Study

Organisms: Homo sapiens

SOPs: No SOPs

Data files: CSV (Blanchard1983a), PNG (Blanchard1983a)

Snapshots: No snapshots

Created: 19th Jul 2019 at 13:57, Last updated: 19th Jul 2019 at 13:59

Digitized pharmacokinetics data (Tanaka2014)

Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF)

Data digitized from publication.

Tanaka2014 Description

Submitter: Matthias König

Assay type:

Technology type:

Investigation: MM-PLF: Multiscale modeling for personalized li...

Study: PKDB Caffeine Study

Organisms: Homo sapiens

SOPs: No SOPs

Data files: CSV (Tanaka2014), PNG (Tanaka2014)

Snapshots: No snapshots

Created: 19th Jul 2019 at 13:57, Last updated: 19th Jul 2019 at 13:59

Digitized pharmacokinetics data (Perera2011)

Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF)

Data digitized from publication.

Perera2011 Description

Submitter: Matthias König

Assay type:

Technology type:

Investigation: MM-PLF: Multiscale modeling for personalized li...

Study: PKDB Caffeine Study

Organisms: Homo sapiens

SOPs: No SOPs

Data files: CSV (Perera2011), PNG (Perera2011)

Snapshots: No snapshots

Created: 19th Jul 2019 at 13:57, Last updated: 19th Jul 2019 at 13:59

Digitized pharmacokinetics data (Magnusson2008)

Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF)

Data digitized from publication.

Magnusson2008 Description

Submitter: Matthias König

Assay type:

Technology type:

Investigation: MM-PLF: Multiscale modeling for personalized li...

Study: PKDB Caffeine Study

Organisms: Homo sapiens

SOPs: No SOPs

Data files: CSV (Magnusson2008), PNG (Magnusson2008)

Snapshots: No snapshots

Created: 19th Jul 2019 at 13:57, Last updated: 19th Jul 2019 at 13:59

Digitized pharmacokinetics data (Hetzler1990)

Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF)

Data digitized from publication.

Hetzler1990 Description

Submitter: Matthias König

Assay type:

Technology type:

Investigation: MM-PLF: Multiscale modeling for personalized li...

Study: PKDB Caffeine Study

Organisms: Homo sapiens

SOPs: No SOPs

Data files: CSV (Hetzler1990), PNG (Hetzler1990)

Snapshots: No snapshots

Created: 19th Jul 2019 at 13:57, Last updated: 19th Jul 2019 at 13:59

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