The George M. O'Brien Michigan Kidney Translational Core Center (MKTC)
Summary
The George M. O’Brien Michigan Kidney Translational Core Center (MKTC) was established to assist investigators and clinicians worldwide in kidney disease research. Their core objective is to enable muti-omic multi-scalar data integration. MKTC consists of two Biomedical Cores: The Applied Systems Biology Core (ASBC) and Data Analytics Services Core (DASC). They provide specialized core services as well as user-friendly tools to enable kidney researchers and trainees to apply to their work.
Applied Systems Biology Core (ASBC)
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Description
The Applied Systems Biology Core (ASBC) primary role is to empower national kidney researchers to analyze, integrate and extract pertinent knowledge from multi-omic datasets (genetic, transcriptomic, epigenomic, metabolomic, proteomic data) from model systems and human studies in support of their individual research needs.
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Services
- Animal Transcript driven data-mining workflow - Bulk RNA Sequencing analysis pipeline
- Animal Transcript driven data-mining workflow - Molecular pathway analysis pipeline
- Animal Transcript driven data-mining workflow - Single cell/single nuc RNA Sequencing analysis pipeline
- CELLxGENE - data extraction service
- CELLxGENE - training
- Clinical and molecular interactions in investigators' data sets
- Conference, meeting abstract preparation
- Conference, meeting presentation support
- General bioinformatic tool training (e.g. R)
- General data result interpretation and discussion, development of next steps
- General troubleshooting
- Grant support - LOS
- Grant support - Writing
- Human Transcript driven data-mining workflow - Bulk RNA Sequencing analysis pipeline
- Human Transcript driven data-mining workflow - Molecular pathway analysis pipeline
- Human Transcript driven data-mining workflow - Single cell/single nuc RNA Sequencing analysis pipeline
- Initial study design consultation
- Metabolomics data-mining workflow - Molecular pathway analysis pipeline
- Metabolomics driven analysis workflow
- Michigan Manuscript development
- Model systems studies to identify pathways shared cross-species
- Multi-scalar data analysis and integration, including cross-species comparison
- Nephroseq - data extraction service
- NephroSeq training
- Protein data-mining workflow - Molecular pathway analysis pipeline
- Protein data-mining workflow - proteomics data analysis pipeline
- Quantitative morphometric analyses of kidney biopsy samples
- Shared Data Mining Services - Initial study design consultation
- Spatial metabolomics service (sample process and data analysis)
- Structured RNA-DNA sequence data integration
- Transcript driven data analysis - Bulk RNA sequencing analysis pipeline
- Transcript driven data analysis - Molecular pathway analysis pipeline
- Transcript driven data-mining workflow - Bulk RNA Sequencing analysis pipeline
- Transcript driven data-mining workflow - Single cell/single nuc RNA Sequencing analysis pipeline
- Transcript driven data-mining workflow - Streamlined self-organizing map (SOM) to identify functional subgroups
- Transcript driven data-mining workflow - Weighted Correlation Network Analysis (WGCNA) to identify co-expressed molecular elements within datasets
- TranSMART CProbe - data extraction service
- TranSMART CProbe - training
- TranSMART CureGN - data extraction service
- TranSMART CureGN - training
- TranSMART NEPTUNE - data extraction service
- TranSMART NEPTUNE - training
- Vitessce - data extraction service
- Vitessce - training
Data Analytic Services Core (DASC)
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Description
The Data Analytic Services Core (DASC) provides access to unique sets of data through distinct data analysis platforms. The database is updated quarterly to provide investigators with quick and easy access to all the data being generated as part of the Center and their web portals include sophisticated and user-friendly analytic tools that allow for mining of these datasets.
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Services
- CELLxGENE - access/support
- Conference, meeting abstract preparation
- Conference, meeting presentation support
- Develop generalized workflow for integrative web-based analysis
- Grant support - LOS
- Grant support - Writing
- Investigating biomarker association (gene, protein, metabolite level) in clinical existing cohorts through TranSMART instance
- Michigan Manuscript development
- Nephroseq - access/support
- TranSMART CProbe - access/support
- TranSMART CureGN - access/support
- TranSMART NEPTUNE- access/support
- Vitessce - access/support
Contact Information
If you would like more information regarding services provided by MKTC, please contact:
Wenjun Ju
wenjunj@med.umich.edu
Website