iRhythmics
OverviewThe 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.
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
Public web page: Not specified
Organisms: Homo sapiens, Mus musculus
FAIRDOM PALs: No PALs for this Project
Project created: 15th Sep 2015
Related items
Projects: iRhythmics
Institutions: Rostock University Medical Centre
Projects: iRhythmics
Institutions: Rostock University Medical Centre
Projects: iRhythmics
Institutions: Leibniz Institute for Farm Animal Biology (FBN)
https://orcid.org/0000-0002-7968-3152
Projects: iRhythmics
Institutions: University of Rostock
Projects: iRhythmics
Institutions: Leibniz Institute for Farm Animal Biology (FBN)
https://orcid.org/0000-0003-2018-2836
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: Rostock University Medical Centre
https://orcid.org/0000-0001-6287-4916
Projects: iRhythmics
Institutions: University Medicine of Greifswald
Projects: COSMIC, BaCell-SysMO, SYSTERACT, HUMET Startup, INCOME, BESTER, iRhythmics
Institutions: University of Rostock
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.
Person responsible: Anne-Marie Galow
Snapshots: No snapshots
This study contains our single nuclei characterisation of whole hearts from Fzt.DU mice published in Cells.
Contributor: Anne-Marie Galow
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Contributor: Markus Wolfien
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
This file contains the top 100 transcripts for the identified cell types in the integrated dataset.
Creator: Anne-Marie Galow
Contributor: Anne-Marie Galow
DownloadThe file contains the absolute cell numbers per cluster for each individual dataset used in the integrated analysis.
Creator: Anne-Marie Galow
Contributor: Anne-Marie Galow
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
Contributor: Markus Wolfien
This dot-plot represents only the most significant genes per identified cell type cluster.
Creators: Markus Wolfien, Anne-Marie Galow
Contributor: Markus Wolfien
This file contains the top markers for the identified cell types.
Creators: Markus Wolfien, Anne-Marie Galow
Contributor: Markus Wolfien
This pdf contains the top 10 markers for each identified cell type as a dot-plot.
Creators: Markus Wolfien, Anne-Marie Galow
Contributor: Markus Wolfien
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
Contributor: Markus Wolfien
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
Contributor: Markus Wolfien
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
Contributor: Markus Wolfien
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
Contributor: Anne-Marie Galow
This file contains the detailed experimental protocol to isolate nuclei from murine hearts.
Creators: Markus Wolfien, Anne-Marie Galow
Contributor: Markus Wolfien
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
Contributor: Markus Wolfien
The file contains an UMAP representation illustrating the expression of the stem cell marker Cd34 in all identified cell clusters.
Creator: Anne-Marie Galow
Contributor: Anne-Marie Galow
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
Contributor: Markus Wolfien
This file contains a detailed description of the underlying experimental procedure and the computational analysis.
Creators: Markus Wolfien, Anne-Marie Galow
Contributor: Markus Wolfien
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
Contributor: Markus Wolfien
