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- Markus Wolfien
SEEK ID: https://fairdomhub.org/people/577
Location:
Germany
Expertise: Bioinformatics, Transcriptomics, RNA-Seq, AI, Data Integration
Related items
- Projects (2)
- Institutions (1)
- Investigations (0+5)
- Studies (3+9)
- Assays (3+13)
- Data files (8+16)
- SOPs (3+3)
- Presentations (0+2)
- Events (0+1)
- Documents (3+2)
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
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Programme: Independent Projects
Public web page: https://irhythmics.med.uni-rostock.de/
Organisms: Homo sapiens, Mus musculus
The gut–brain axis (GBA) provides a bidirectional homeostatic communication between the gastrointestinal tract and the central nervous system. The interdisciplinary collaboration is going to fully explore a first comprehensive GBA cross-disease map of genetic, expression and regulatory changes associated with ulcerative colitis and schizophrenia disease entities.
Dysfunction of this axis can have pathophysiological consequences. Genome-wide association studies (GWAS) have identified >300
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Programme: This Project is not associated with a Programme
Public web page: https://www.sbi.uni-rostock.de/research/projects/detail/49
Start date: 1st Feb 2019
End date: 12th Feb 2019
Organisms: Not specified
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
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
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...
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
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: 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
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