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We constructed a logic-based model to unravel mechanisms underlying pancreatic cancer and fibrosis. Model was calibrated with expression data and simulated for stimulus response and perturbation analysis to identify disease markers. Disease markers predicted by the model are validated through patient data using KM survival plot (which stratify patient into short and long survival) and box plot (expression level of the markers in normal vs. pancreatic patients). In vitro validations of the model ...

Testing data upload

Creator: Chris Wilson

Submitter: Chris Wilson

Visualization of the workflow demonstrating a step-by-step explanation for a sc-SynO analysis. a) Several or one snRNA-Seq or scRNA-Seq fastq datasets can be used as an input. Here, we identify our cell population of interest and provide raw or normalized read counts of this specific population to sc-SynO for training. b) Further information for cluster annotation and processed count data are serving as input for the core algorithm. c) Based on the data input, we utilize the LoRAS synthetic ...

Validation of the sc-SynO model for the first use case of cardiac glial cell annotation. UMAP representation of the manually clustered Bl6 dataset of Wolfien et al. (2020) Precicted cells of sc-SynO are highlighted in blue, cells not chosen are grey. UMAP representation of the manually clustered dataset of Vidal (2019). Precicted cells of sc-SynO are highlighted in blue, cells not chosen are grey. Average expression of the respective top five cardiac glial cell marker genes for both validation ...

Validation of the sc-SynO model for the second use case of proliferative cardiomyocytes annotation. a) UMAP representation of the manually clustered single-nuclei dataset of Linscheid et al. (2019) Precicted cells of sc-SynO are highlighted in blue (based on top 20 selected features in the training model), red (based on top 100 selected features in the training model) cells not chosen are grey. b) UMAP representation of the manually clustered dataset of Vidal et al. (2020). PPrecicted cells of ...

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Creator: Huseyin Tas

Submitter: Huseyin Tas

This pdf file contains all figures of the article "Integrative Cluster Analysis of Whole Hearts Reveals Proliferative Cardiomyocytes in Adult Mice" in high resolution.

This pdf contains the top 10 markers for each identified cell type as a dot-plot.

The file contains an UMAP representation illustrating the expression of the stem cell marker Cd34 in all identified cell clusters.

The file contains FeaturePlots of 4 different cardiomyocyte markers (Actn2, Tnnc1, Actc1 and Ryr2) to demonstrate how annotation of clusters needs to be based on several markers and approaches, which in the aggregate allow for more reliable conclusions/results.

The file contains the absolute and relative cell/nuclei numbers per cluster for each individual dataset used in the integrated analysis. Subpopulations were grouped together for the representation of relative cell/nuclei numbers.

This file contains the top 100 transcripts for the identified cell types in the integrated dataset.

File contains the detailed cluster names for each data set, number of nuclei per cluster, average reads per nucleus, and average reads per cluster.

Creator: Markus Wolfien

Submitter: Markus Wolfien

This dot-plot represents only the most significant genes per identified cell type cluster.

This file contains the top markers for the identified cell types.

This pdf contains the top 10 markers for each identified cell type as a dot-plot.

This file contains the R-script to analyse single nuclei data previously processed with kallisto and bustools. The analyses utilizes the Seurat, harmony and RNAvelocity package.

This file contains the detailed UNIX commands for mm10 index file creation (suitable for RNAvelocity) for kallisto as well as the commands used for the alignment with kallisto and the subsequent quantification with bustools.

This file contains the IDs, adj. p-values and official gene names of the top 100 marker genes (where applicable) for each of the identified cluster.

Creator: Markus Wolfien

Submitter: Markus Wolfien

Contains time series metabolomics measurements in mM from different experiments. Measurements of these internal metabolites should be combined with Growth curve A measurements forthe external metabolites. Contains mean and standard deviation for a few but not all mutants based on multiple time series experiments carried out over the years. Daniel 3rd experiment data is the most complete and is together with Wodke and Tobias measurements used as training data for the model.

Contains for all samples, mean metabolite concentration and shows enzyme concentration used in model fitting and simmulations. Only metabolite present in the model are shown.

Simulation of double mutants and perturbations and time series samples using for Sample 1 only OE mutants of which we update the enzyme concentrations. For each second mutant the enzyme concentrations in case of OE and KO mutants in updated and the metabolite concentrations of the second sample are loaded in the model. Using this approach the model approximately predicts combinatorial effects of OE mutations with other mutations, perturbations and time series concentrations.

Comparison of model SS metabolite concentrations with measured values using 1000x sampling from the Gausian distribution of the measured values based on multiple replicates per measured conditions. Graphs showing the distribution of measured and simulated metabolite concentration for 95 mutand (KO, OE), perturbation and time series measurements. Model simulations performed using 24h proteomics with modification of enzyme parameters for KO and OE mutants.

Contains: -Relative metabolite measurements at different time points from all experiments -Absolute metabolite measurements for amino-acid analysis of the proteome and the cytosol -Effect on adding CaCl2, KCl or NaCl to the medium on growth -Effect of spiking of growth medium with additional amino acids

Contains all 10 parameter sets, loaded with proteomics measurements for three time points (6h,24h, 48h). Contains all parameter sets exported from COPASI, an overview of the parameter sets in the three conditions and how well they perform as well as scripts to load parameter sets as well as an R script to generate an overview of the model error in predicting for all 10 parameter sets.

Contains a Jupyter notebook file that uses libroadrunner and tellurium to run all simmulations and analysis based on the 40 independent samples. The Readme.txt file contains information on how to recreate the complete modelling environment used for all simmulations and analysis using Anaconda.

Local sensitivity analysis based on 40 samples using 1000x sampling from measurement distribution. The control shown is the control over flux through glycolysis represented by flux through PRK. Th plot summarized the control for each parameter over all observed metabolite concentrations encountered for the 40 samples. As such the metabolic control analysis is local but shows the distribution taking into account measurement error as well as biological variation over the 40 samples.

Tab seperated file containing the raw output of the local sensitivity analysis based on 40 samples (based on 1000x sampled metabolite values) from the MEAN and SD of the metabolite measurements. Sensitivity analysis is based on the flux through PFK as objective and as proxy for flux through glycolysis. Data can be plotted using the R script "plotLocalGlobalSensitivity1.5.R" associated to the same assay.

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