Data files

Experimental data set for the kinetic characterisation of G3PDH

Kinetic characterisation of GAPDH. Expermental data for enzyme reaction rates with increasing concentrations of BPG, NADPH, NADP, GAP and Pi.

Experimental data set for the kinetic characterisation of GAPDH

Simulation results of GAPDH experimental data for BPG, NADPH, NADP, GAP, and Pi

Pure cultures of P. cordatum were grown at 20°C, 26°C and 30°C until exponential and stationary growth phase and were harvested for metabolite extraction.

Online metabolite derivatization was performed using a Gerstel MPS2 autosampler (Muehlheim, Germany). Dried metabolites were dissolved in 15 µl of 2 % methoxyamine hydrochloride in pyridine at 40 °C under shaking. After 90 min, an equal volume of N-Methyl-N-(trimethylsilyl)trifluoroacetamide (MSTFA) was added and held for 30 min at 40 °C. One ...

GCN4

Prepared (sub-)cellular fractions were separated by gradient SDS-PAGE and entire sample lanes cut into pieces prior to in-gel digest and nanoLC separation coulpled to iontrap MS/MS detection.

For each module, GSEA analysis was conducted by using web-tool g:profiler and only biological process (BP) were retained. Parameters for GSEA are default.

In this study, we used publically available dataset from gene expression omnibus (GEO):

Transcriptomic analysis of liver biopsies that cover the spectrum of nonalcoholic fatty liver disease reveals genes that are progressively regulated over the course of the disease. This study demonstrates that progressive changes in expression of these genes can be used to approximate the histological grade of a liver biopsy. Furthermore, the relative progression profiles of these disease-responsive genes are ...

This data file shows results from the different chemostat experiments.Gene expression rates are presented.

There are four datasheets in the Excel file: 1. Gene pattern and the corresponding category (the gene list is then divided into the other three datasheets); 2. These gene names (patterns) can be directly followed by either a letter or a number; 3. These gene names (patterns) should be directly followed by a letter; 4. These gene names (patterns) should be directly followed by a number.

We obtained PE associated microRNA based on previously mentioned experiments. miRTarBase v8.0 was used to identify gene targets and extract 1000 miRNA - gene pairs with 667 unique genes (Huang et al., 2020). miRTarBase is a database for experimentally validated miRNA-target interactions. To minimize false positives only strong-evidence miRNA-target pairs were considered.

We obtained PE associated microRNA based on previously mentioned experiments. miRTarBase v8.0 was used to identify gene targets and extract 1000 miRNA - gene pairs with 667 unique genes (Huang et al., 2020). miRTarBase is a database for experimentally validated miRNA-target interactions. To minimize false positives only strong-evidence miRNA-target pairs were considered.

Information for salmon genes, including transcript length used for calculating transcrip per million (TPM) value

Additional File 1

We performed network analysis to investigate the dysregulated biological processes in the disease progression and revealed the molecular mechanism underlying NAFLD C57BL/6J mice were fed a standard mouse chow diet and housed in a 12‐h light–dark cycle. From the age of 8 weeks, the mice were then divided into two groups of 5 mice fed with chow diet, 4 mice fed with high-sucrose diet for 3 weeks, respectively. At the age of 11 weeks, we performed a genome-wide transcriptomic analysis on tissue ...

This template is for recording genome data from the NimbleGen platform. 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 these templates will mean easier submission to GEO/ArrayExpress and greater consistency of data in SEEK.

Global microRNA expression profiling of high-risk ER+ breast cancers from patients receiving adjuvant Tamoxifen mono-therapy: a DBCG study

GEO Data set GSE9893 : A gene expression signature predicting the recurrence of tamoxifen-treated primary breast cancer.

_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_GAtreat/

Instructions and database scripts for extracting COVID-19 related data from i2b2

Data sheet from the Neves et al JBC, 2002 publication. Used as a test data set for data upload.

Experimental data set for the kinetic characterisation of the glucose transport reaction

Data for global pH monitoring experiments for precipitation in publication: Microbial-induced calcium carbonate precipitation: An experimental toolbox for in situ and real-time investigation of micro-scale pH evolution. Included data: calibration data and data for pH evolution of precipitation process (including spectrum before measurement, timeevolution of absorption intensity and spectrum after measurement).

Violin plot of the metabolic control of model parameters on the flux through PFK (as a proxy for flux through glycolysis) based on a 100.000 Latin Hypercube samples from the parameter space (range 0.001-100 for Km values and 0.001-1000 for Vmax values).

Shows the correlation in metabolic control between parameters. The plot shows central carbon metabolis basically consist of a few control hubs of reactions of which the parameters are correlated. In other words, just the reaction network combined with allosteric control and equilibrium constants impose some constrains on possible parameter value combinations that lead to certain behaviour (such as the flux and concentrations measured in vivo/vitro).

Contains the raw output of the global sensitivity analysis, can be used as input for plotting using the R script "plotLocalGlobalSensitivity1.5.R" associated to the same asset

Glucose pulsed L. lactis with 20 mM glucose in 100 mM MES buffer at pH 6.5 and followed intracellular metabolites in time

L. lactis was grown in LAB medium, strongly concentrated and glucose-pulsed in a MES buffer. Intracellular metabolite concentration is followed in time.

Glucose pulsed S pyogenes with 5 mM glucose in 100 mM MES buffer at pH 6.5 and followed intracellular metabolites in time

Consensus between selected mapping methods.

related to Figure 6 and additional file 6

identified gene targets were used as input on the gProfiler website. Ontology and pathway GO terms with an adjusted p-value <0.05 were considered significantly overrepresented.

L. lactis cultures were grown at different dilution rates in glucose-limited chemostat conditions and were analyzed with respect to physiological parameters. Amino acid consumption, glucose consumption and production of fermentation products were measured in steady-state conditions,

Measurement of by-product formation rates, substrate consumption rates and extracellular concentrations of cAMP under aerobic batch conditions with glucose as substrate.

Measurement of by-product formation rates, substrate consumption rates and extracellular concentrations of cAMP under anaerobic batch conditions with glucose as substrate.

This is the fatty acid profile data from the freshwater portion of the feed switch trial. eg: D0_MA_M_6 (Day 0, MA- Marine oil, L-liver, fish number 6)

Fatty acid Systematic Name C14:0 Myristic acid myristin-syre C16:0 Palmitic acid palmitin-syre C16:1n7 Palmitoleic palmitolein-syre C17:0 C17:1 C18:0 stearic acid stearin-syre 18:1n9c oleic acid olje-syre C18:2n6c linoleic acid linolsyre C20:1 eicosenoic acid C18:3n3 linolenic acid linolensyre C20:2 eicosadienoic C22:1 cetoleic acid cetolein-syre ...

This is the fatty acid profile data from the seawater portion of the feed switch trial. eg: D0_MA_M_6 (Day 0, MA- Marine oil, Muscle, fish number 6)

Fatty acid Systematic Name C14:0 Myristic acid myristin-syre C16:0 Palmitic acid palmitin-syre C16:1n7 Palmitoleic palmitolein-syre C17:0 C17:1 C18:0 stearic acid stearin-syre 18:1n9c oleic acid olje-syre C18:2n6c linoleic acid linolsyre C20:1 eicosenoic acid C18:3n3 linolenic acid linolensyre C20:2 eicosadienoic C22:1 cetoleic acid cetolein-syre ...

Read counts for each sample

CPM is a descriptive measures for the expression level of a gene.

FPKMs or Fragments Per Kilobase of exon per Million reads . Fragment means fragment of DNA, so the two reads that comprise a paired-end read count as one. Per kilobase of exon means the counts of fragments are then normalized by dividing by the total length of all exons in the gene (or transcript). This bit of magic makes it possible to compare Gene A to Gene B even if they are of different lengths. Per million reads means this value is then normalized against the library size. This bit of magic ...