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The project addresses the generation and establishment of programmed pacemaker cells for an in vitro drug testing possibility to perform predictive tests. This may lead to an improved treatment of cardiac arrhythmias or an accurate identification of potential drug molecules at a very early stage of development. Important benefits will arise in verifying the safety of a wide variety of medicines while reducing animal testing. For more information you may visit our project website at https://irhythmics.med.uni-rostock.de/.
This project is funded by the European Social Fund (ESF) program of the European Union (ESF/14-BM-A55-0027).
Programme: Independent Projects
SEEK ID: https://fairdomhub.org/projects/28
Funding codes:- ESF/14-BM-A55-0027
Public web page: https://irhythmics.med.uni-rostock.de/
Organisms: Homo sapiens, Mus musculus
FAIRDOM PALs: No PALs for this Project
Project created: 15th Sep 2015
Related items
- People (19)
- Institutions (4)
- Investigations (0+5)
- Studies (3+11)
- Assays (5+16)
- Data files (16+28)
- Models (2)
- SOPs (4+12)
- Presentations (0+9)
- Events (0+2)
- Documents (17+25)
Projects: iRhythmics
Institutions: Rostock University Medical Centre
Projects: iRhythmics
Institutions: Leibniz Institute for Farm Animal Biology (FBN)
Projects: iRhythmics
Institutions: Rostock University Medical Centre
Projects: iRhythmics
Institutions: Leibniz Institute for Farm Animal Biology (FBN)

Projects: iRhythmics
Institutions: University of Rostock
Roles: PhD Student
Expertise: Machine Learning, Deep Learning
Projects: iRhythmics
Institutions: Leibniz Institute for Farm Animal Biology (FBN)

Projects: iRhythmics
Institutions: Rostock University Medical Centre
Roles: PhD Student
Expertise: Cell biology, Molecular microbiology
Tools: Cell and tissue culture, Cytometry and fluorescent microscopy, electrophysiology
Projects: iRhythmics
Institutions: Rostock University Medical Centre
Roles: Postdoc
Expertise: Cell biology, Image analysis
Tools: super resolution microscopy, iPSC culture, Photoactivated localization microscopy
Projects: iRhythmics
Institutions: Rostock University Medical Centre
Projects: iRhythmics
Institutions: Rostock University Medical Centre
Projects: iRhythmics
Institutions: Rostock University Medical Centre
Projects: iRhythmics
Institutions: Rostock University Medical Centre
Projects: iRhythmics
Institutions: Rostock University Medical Centre

Projects: iRhythmics
Institutions: University Medicine of Greifswald
Projects: iRhythmics
Institutions: Rostock University Medical Centre
Projects: iRhythmics, GB-XMap: Assessing the risk of gut-brain cross-diseases Investigating the gut-brain-axis
Institutions: University of Rostock

Roles: PhD Student
Expertise: Bioinformatics, Transcriptomics, RNA-Seq, AI, Data Integration
Projects: COSMIC, BaCell-SysMO, SYSTERACT, HUMET Startup, INCOME, BESTER, iRhythmics, COVID-19 Disease Map
Institutions: University of Rostock
Expertise: dynamics of biological networks, Data analysis Mathematical modelling Bioinformatics Systems biology, Dynamics and Control of Biological Networks
Tools: Computational and theoretical biology, ODE, Matlab, Mathematica, stimulus response experiments, differential algebraic equations, quantitative western blot analyses, quantitative western blot analysis, Stochastic models
This study includes the single snRNA-seq in whole adult murine hearts from an inbred (C57BL/6NRj) and an outbred (Fzt:DU) mouse strain in comparison to publicly available scRNA-seq data of the tabula muris project.
Investigation: 1 hidden item
Assays: integrative cluster analysis of single cell and single nuclei data
This study contains our single nuclei characterisation of whole hearts from Fzt.DU mice published in Cells.
Investigation: 1 hidden item
Person responsible: Markus Wolfien
Snapshots: Snapshot 1
Investigation: 1 hidden item
Assays: Single nuclei RNA-Seq analysis of Fzt:DU and BL6 mice
Application of the LoRAS oversampling approach on single-cell/single-nuclei data to annotate/identify specific cell populations in new data based on previously, manually curated data.
Investigation: 1 hidden item
Study: 1 hidden item
Organisms: No organisms
Models: Data and Jupyter notebooks for our analysis on ..., Data and Jupyter notebooks for our analysis on ...
SOPs: No SOPs
Data files: Schematic overview of sc-SynO, sc-SynO use case 1: cardiac glial cell identifi..., sc-SynO use case 2: proliferative cardiomyocyte...
Here, we conduct a proof of principle by comparing a 2D and 3D fluorescent image analysis based approach on unlabeled cardiomyocytes. Based on the CellProfiler software, we extracted high-dimensional features of individual cells and nuclei, which are subsequently down-sampled and clustered. These clusters are furthermore benchmarked via different machine learning classifiers (e.g., AdaBoost, Gradient Boosting, Random Forest) as the ground truth for our proposed approach.
Investigation: 1 hidden item
Study: 1 hidden item
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: 1 hidden item
Submitter: Anne-Marie Galow
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Investigation: 1 hidden item
Study: integrative cluster analysis - proliferative ca...
Organisms: No organisms
Models: No Models
SOPs: Nuclei isolation for single nuclei RNA-seq, R-Script for integrative clusteranalysis of sin...
Data files: CD34 expression across clusters, FeaturePlot of cardiomyocyte markers, Figures Galow et al., Top100 transcripts, number of cells per cluster, top10 marker for cell clusters
Investigation: 1 hidden item
Study: Single nuclei characterisation of adult mammali...
Organisms: No organisms
Models: No Models
SOPs: Nuclei isolation for single nuclei RNA-seq
Data files: R script for snRNAseq analysis, Top 10 marker genes per nuclei, Top 100 marker genes for whole heart fzt:DU cel..., Top marker genes per nuclei, UNIX script for snRNAseq
Investigation: 1 hidden item
Study: Single nuclei comparison
Organisms: No organisms
Models: No Models
SOPs: R script for single nuclei analysis, UNIX script for snRNA-Seq processing
Data files: Marker genes for single nuclei clusters, Nuclei characteristics for the single nuclei an...
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
...
Creators: Markus Wolfien, Saptarshi Bej
Submitter: Markus Wolfien
Investigations: 1 hidden item
Studies: 1 hidden item
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
...
Creators: Markus Wolfien, Saptarshi Bej
Submitter: Markus Wolfien
Investigations: 1 hidden item
Studies: 1 hidden item
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
...
Creators: Markus Wolfien, Saptarshi Bej
Submitter: Markus Wolfien
Investigations: 1 hidden item
Studies: 1 hidden item
This pdf file contains all figures of the article "Integrative Cluster Analysis of Whole Hearts Reveals Proliferative Cardiomyocytes in Adult Mice" in high resolution.
Creators: Anne-Marie Galow, Markus Wolfien
Submitter: Anne-Marie Galow
Investigations: 1 hidden item
This pdf contains the top 10 markers for each identified cell type as a dot-plot.
Creator: Anne-Marie Galow
Submitter: Anne-Marie Galow
Investigations: 1 hidden item
The file contains an UMAP representation illustrating the expression of the stem cell marker Cd34 in all identified cell clusters.
Creator: Anne-Marie Galow
Submitter: Anne-Marie Galow
Investigations: 1 hidden item
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.
Creator: Anne-Marie Galow
Submitter: Anne-Marie Galow
Investigations: 1 hidden item
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.
Creator: Anne-Marie Galow
Submitter: Anne-Marie Galow
Investigations: 1 hidden item
This file contains the top 100 transcripts for the identified cell types in the integrated dataset.
Creator: Anne-Marie Galow
Submitter: Anne-Marie Galow
Investigations: 1 hidden item
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
Investigations: 1 hidden item
Studies: Single nuclei comparison
This dot-plot represents only the most significant genes per identified cell type cluster.
Creators: Markus Wolfien, Anne-Marie Galow
Submitter: Markus Wolfien
Investigations: 1 hidden item
This file contains the top markers for the identified cell types.
Creators: Markus Wolfien, Anne-Marie Galow
Submitter: Markus Wolfien
Investigations: 1 hidden item
This pdf contains the top 10 markers for each identified cell type as a dot-plot.
Creators: Markus Wolfien, Anne-Marie Galow
Submitter: Markus Wolfien
Investigations: 1 hidden item
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.
Creators: Markus Wolfien, Anne-Marie Galow
Submitter: Markus Wolfien
Investigations: 1 hidden item
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.
Creator: Markus Wolfien
Submitter: Markus Wolfien
Investigations: 1 hidden item
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
Investigations: 1 hidden item
Studies: Single nuclei comparison
Creator: Saptarshi Bej
Submitter: Markus Wolfien
Model type: Not specified
Model format: Not specified
Environment: Not specified
Organism: Mus musculus
Investigations: 1 hidden item
Studies: 1 hidden item
Modelling analyses: sc-SynO: a LoRAS integration to annotate rare-c...
Creator: Saptarshi Bej
Submitter: Saptarshi Bej
Model type: Not specified
Model format: Not specified
Environment: Not specified
Organism: Not specified
Investigations: 1 hidden item
Studies: 1 hidden item
Modelling analyses: sc-SynO: a LoRAS integration to annotate rare-c...
This file contains the R-script to analyse single nuclei and single cell data of Bl6 and Fzt:DU mice previously processed with cellranger. The analyses utilizes the Seurat and harmony package to integrate three datasets before subsequent downstream analysis characterizing proliferative cardiomyocytes.
Creator: Anne-Marie Galow
Submitter: Anne-Marie Galow
Investigations: 1 hidden item
Creator: Markus Wolfien
Submitter: Markus Wolfien
Investigations: 1 hidden item
Studies: Single nuclei comparison
This file contains the detailed experimental protocol to isolate nuclei from murine hearts.
Creators: Markus Wolfien, Anne-Marie Galow
Submitter: Markus Wolfien
Investigations: 1 hidden item
Studies: Single nuclei characterisation of adult mammali..., integrative cluster analysis - proliferative ca...
Assays: Single nuclei RNA-Seq analysis of Fzt:DU mice, integrative cluster analysis of single cell and...
This R-script contains the single nuclei analysis for our Fzt:DU and BL6 data, namely bustools file integration, preprocessing, scaling, clustering, marker indentification and annotation of markers and RNAvelocity computation.
Creator: Markus Wolfien
Submitter: Markus Wolfien
Investigations: 1 hidden item
Studies: Single nuclei comparison
Creator: Maximilian Hillemanns
Submitter: Maximilian Hillemanns
Investigations: 1 hidden item
Studies: 1 hidden item
Creator: Maximilian Hillemanns
Submitter: Maximilian Hillemanns
Investigations: 1 hidden item
Studies: 1 hidden item
Creator: Maximilian Hillemanns
Submitter: Maximilian Hillemanns
Investigations: 1 hidden item
Studies: 1 hidden item
Creator: Maximilian Hillemanns
Submitter: Maximilian Hillemanns
Investigations: 1 hidden item
Studies: 1 hidden item
Creator: Maximilian Hillemanns
Submitter: Maximilian Hillemanns
Investigations: 1 hidden item
Studies: 1 hidden item
Creator: Maximilian Hillemanns
Submitter: Maximilian Hillemanns
Investigations: 1 hidden item
Studies: 1 hidden item
Creator: Maximilian Hillemanns
Submitter: Maximilian Hillemanns
Investigations: 1 hidden item
Studies: 1 hidden item
Creator: Maximilian Hillemanns
Submitter: Maximilian Hillemanns
Investigations: 1 hidden item
Studies: 1 hidden item
Creator: Maximilian Hillemanns
Submitter: Maximilian Hillemanns
Investigations: 1 hidden item
Studies: 1 hidden item
Creator: Maximilian Hillemanns
Submitter: Maximilian Hillemanns
Investigations: 1 hidden item
Studies: 1 hidden item
Creator: Maximilian Hillemanns
Submitter: Maximilian Hillemanns
Investigations: 1 hidden item
Studies: 1 hidden item
Creator: Maximilian Hillemanns
Submitter: Maximilian Hillemanns
Investigations: 1 hidden item
Studies: 1 hidden item
Creator: Maximilian Hillemanns
Submitter: Maximilian Hillemanns
Investigations: 1 hidden item
Studies: 1 hidden item
A CellProfiler pipeline for 3D analysis of cardiomyocytes
Creator: Maximilian Hillemanns
Submitter: Maximilian Hillemanns
Investigations: 1 hidden item
Studies: 1 hidden item
Sehr geehrte Damen und Herren,
mit diesem Informationsflyer erfahren Sie mehr über das iRhythmics Projekt unseres Konsortiums.
Mit freundlichen Grüßen
Anna Skorska
Projektmanagerin iRhythmics
Creator: Anna Skorska
Submitter: Markus Wolfien
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
This file contains a detailed description of the underlying experimental procedure and the computational analysis.
Creators: Markus Wolfien, Anne-Marie Galow
Submitter: Markus Wolfien
Investigations: 1 hidden item
Studies: Single nuclei comparison
This PDF contains a dotplot indicating the gene expression of the top 100 markers (where applicable) for each of the identified 23 clusters.
Creator: Markus Wolfien
Submitter: Markus Wolfien
Investigations: 1 hidden item
Studies: Single nuclei comparison