Data files

Prorocentrum cordatum was subjected to whole cell shotgun analyses (in-solution digest) unsing nanoLC ESI-intrap MS/MS

Linked with Model: 10.15490/fairdomhub.1.model.802.1

Linked with model: DOI: 10.15490/fairdomhub.1.model.801.1

Linked to model: DOI: 10.15490/fairdomhub.1.model.799.1

Linked to model: DOI: 10.15490/fairdomhub.1.model.800.1

Linked with model: 10.15490/fairdomhub.1.model.802.1

Linked with model: 10.15490/fairdomhub.1.model.802.1

Linked with model: 10.15490/fairdomhub.1.model.802.1

Linked with model: 10.15490/fairdomhub.1.model.802.1

Linked with Model: 10.15490/fairdomhub.1.model.802.1

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

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 ...

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.

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