The George M. O’Brien Kidney Resource Alliance (OKRA) provides roughly 400 specialized resources, tools, technologies, services, and expertise beyond those typically available in an individual lab or institutional core. If you are interested in requesting any of the resources below, please click the “Request Here” button below. If you have any questions, email us at okrancc@uab.edu:
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Animal Models/Procedures
Animal/material transfer Indiana University Intravital core/Molecular Imaging Resource cores Rodent cisplatin kidney injury Indiana University Intravital core/Molecular Imaging Resource cores Rodent Kidney Ischemia reperfusion injury Indiana University Intravital core/Molecular Imaging Resource cores Rodent Nephrectomy Indiana University Intravital core/Molecular Imaging Resource cores Rodent sepsis models Indiana University Intravital core/Molecular Imaging Resource cores Comprehensive mouse kidney phenotyping for diet and stress mechanisms Johns Hopkins University Biomedical Resource Core (B-DSSL) Germ-free facility consultation use Johns Hopkins University Biomedical Resource Core (B-DSSL) Germ-free sample banks Johns Hopkins University Biomedical Resource Core (B-DSSL) GFR measurements Johns Hopkins University Biomedical Resource Core (B-DSSL) Humanized mouse diet protocols Johns Hopkins University Biomedical Resource Core (B-DSSL) Immunological manifestations of dietary and social stressors in the kidney Johns Hopkins University Biomedical Resource Core (B-DSSL) Isolated Nephron segment Ex Vivo Analysis Johns Hopkins University Biomedical Resource Core (B-DSSL) Kidney Slice Preparation Johns Hopkins University Biomedical Resource Core (B-DSSL) Metabolic Cage and Clearance Studies Johns Hopkins University Biomedical Resource Core (B-DSSL) Metabolism phenotyping Johns Hopkins University Biomedical Resource Core (B-DSSL) Mouse biobank of dietary and social stress models Johns Hopkins University Biomedical Resource Core (B-DSSL) Optical Clearing Johns Hopkins University Biomedical Resource Core (B-DSSL) Plasma and Urine Electrolyte Panels Johns Hopkins University Biomedical Resource Core (B-DSSL) Protocols, training, and service to isolate and characterize kidney immune cells by flow cytometric analysis (FACS) Johns Hopkins University Biomedical Resource Core (B-DSSL) Small Sample RNAseq in Isolated Nephron Segments Johns Hopkins University Biomedical Resource Core (B-DSSL) Telemetric Blood pressure Monitoring Johns Hopkins University Biomedical Resource Core (B-DSSL) Cell-type specific target expression and distribution assessment NU-USC Resource Development Core 5/6th nephrectomy (both steps) UAB-UCSD Pre-Clinical Core Aorta TX UAB-UCSD Pre-Clinical Core Automated tail-cuff blood pressure determination (each, 6 days) UAB-UCSD Pre-Clinical Core Blodd/Urine Collection UAB-UCSD Pre-Clinical Core Cannulation (indwelling with injection port) UAB-UCSD Pre-Clinical Core Determination of GFR in awake rodents UAB-UCSD Pre-Clinical Core Fistula UAB-UCSD Pre-Clinical Core GFR (transcutaneous FITC-sinistrin) in rodents UAB-UCSD Pre-Clinical Core IP Injection UAB-UCSD Pre-Clinical Core Kidney ischemia/reperfusion (IRI) UAB-UCSD Pre-Clinical Core Kidney TX UAB-UCSD Pre-Clinical Core Laser Capture Microdissection from frozen tissue (~70 pieces individually collected per sample; sample quality and amount appropriate for RNA-Seq or potentially proteomics) UAB-UCSD Pre-Clinical Core Metabolic cage experiments in mice (per animal and week) UAB-UCSD Pre-Clinical Core Micropuncture for nephron function and TG feedback UAB-UCSD Pre-Clinical Core Misc. surgical services involving body wall penetration (per hour) UAB-UCSD Pre-Clinical Core Orthotopic kidney transplantation UAB-UCSD Pre-Clinical Core Osmotic pump implant UAB-UCSD Pre-Clinical Core Parabiosis (mice) UAB-UCSD Pre-Clinical Core Radio-telemetry determination of blood pressure UAB-UCSD Pre-Clinical Core Tail vein injection or venipuncture (per animal) UAB-UCSD Pre-Clinical Core Thymectomy UAB-UCSD Pre-Clinical Core Tissue Harvest UAB-UCSD Pre-Clinical Core Tissue oxygen partial pressure determination in kidney UAB-UCSD Pre-Clinical Core Unilateral Ureteral Obstruction UAB-UCSD Pre-Clinical Core Whole kidney clearance/oxygen consumption studies UAB-UCSD Pre-Clinical Core Model systems studies to identify pathways shared cross-species University of Michigan Applied Systems Biology Core Animal Handling and Husbandry University of Pittsburgh Model Systems Core Animal Models - Blood pressure telemetry University of Pittsburgh Model Systems Core Animal Models - Injury biomarker assessment University of Pittsburgh Model Systems Core Animal Models - Measurement of GFR and RBF University of Pittsburgh Model Systems Core Animal Models - Metabolic cage studies, urine metabolites University of Pittsburgh Model Systems Core Animal Models - Mitochondrial / Bioenergetics (Seahorse) University of Pittsburgh Model Systems Core Animal Models - Purine metabolomics University of Pittsburgh Model Systems Core Animal Models - Real-time super-resolution ultrasound of kidney microvasculature University of Pittsburgh Model Systems Core Animal Models - Tissue Harvesting University of Pittsburgh Model Systems Core Disease Models: AKI (cecal ligation and puncture) University of Pittsburgh Model Systems Core Disease Models: AKI (cisplatin nephrotoxicity) University of Pittsburgh Model Systems Core Disease Models: AKI (gentamicin nephrotoxicity) University of Pittsburgh Model Systems Core Disease Models: AKI (ischemia-reperfusion injury) University of Pittsburgh Model Systems Core Disease Models: AKI (sickle cell crisis) University of Pittsburgh Model Systems Core Disease Models: CKD University of Pittsburgh Model Systems Core Disease Models: CKD (chronic angiotensin II infusion) University of Pittsburgh Model Systems Core Disease Models: CKD (FSGS) University of Pittsburgh Model Systems Core Disease Models: CKD (genetic models) University of Pittsburgh Model Systems Core Disease Models: CKD (two kidney one clip hypertension) University of Pittsburgh Model Systems Core Disease Models: CKD (unilateral ureteral obstruction) University of Pittsburgh Model Systems Core Epithelial Models - Mammalian cell culture models (proximal tubule, collecting duct, polarized epithelia) University of Pittsburgh Model Systems Core Epithelial Models - Organoid models to study kidney injury University of Pittsburgh Model Systems Core Epithelial Models - Organoid models to study kidney physiology University of Pittsburgh Model Systems Core Epithelial Models - Organoid models to study nephron development University of Pittsburgh Model Systems Core Special Rodent Diets (low and high Na+ and K+) University of Pittsburgh Model Systems Core Yeast Models - Bioinformatic analysis of genotype-phenotype correlations (TopMed, Clinvar, UK BioBank) University of Pittsburgh Model Systems Core Yeast Models - Computational identification of functional variants University of Pittsburgh Model Systems Core Yeast Models - Positive genetic selection assays University of Pittsburgh Model Systems Core Yeast Models - Protein quality control (degradation, ubiquitylation) assays University of Pittsburgh Model Systems Core Yeast Models - Protein trafficking assays (immunofluorescence, density centrifugation) University of Pittsburgh Model Systems Core Generation of primary cells for Seahorse or stable isotope studies WashU Metabolism Core Stable isotope tracing studies in vivo: 15N-glutamine: data provisioning WashU Metabolism Core Stable isotope tracing studies in vivo: branched chain amino acids: data provisioning WashU Metabolism Core Analysis of VUS in non-COL4A genes through generation and analysis of gene edited models WashU Variant Validation Core COL4A3/A4/A5 VUS analysis in vivo by mouse gene editing WashU Variant Validation Core -
Biostatistics/Bioinformatics
Data analysis and visualization Indiana University Intravital core/Molecular Imaging Resource cores Data cleaning, filtering and mapping Indiana University Molecular Imaging Resource core Bioinformatic Analysis Johns Hopkins University Biomedical Resource Core (B-DSSL) Biostatistical support (including clinical trials, epidemiological cohorts, case-control studies, survey data, and -omics studies) Johns Hopkins University Biomedical Resource Core (C-DSSL) Cell surfaceome lentiviral CRISPR gRNA library NU-USC Resource Development Core NGS data analysis (CRISPR gRNA enrichment assessment) NU-USC Resource Development Core AKI Study Analysis and Interpretation UAB-UCSD Clinical Core Analyses of study results UAB-UCSD Clinical Core Analysis of pilot data UAB-UCSD Clinical Core Methodologies and Applications of Artificial Intelligence and Digital Health: AI computing resource UAB-UCSD Clinical Core Sample size and/or power analysis UAB-UCSD Clinical Core Animal Transcript driven data-mining workflow - Bulk RNA Sequencing analysis pipeline University of Michigan Applied Systems Biology Core Animal Transcript driven data-mining workflow - Molecular pathway analysis pipeline University of Michigan Applied Systems Biology Core Animal Transcript driven data-mining workflow - Single cell/single nuc RNA Sequencing analysis pipeline University of Michigan Applied Systems Biology Core CELLxGENE- data extraction service University of Michigan Applied Systems Biology Core Human Transcript driven data-mining workflow - Bulk RNA Sequencing analysis pipeline University of Michigan Applied Systems Biology Core Human Transcript driven data-mining workflow - Molecular pathway analysis pipeline University of Michigan Applied Systems Biology Core Human Transcript driven data-mining workflow - Single cell/single nuc RNA Sequencing analysis pipeline University of Michigan Applied Systems Biology Core Metabolomics data-mining workflow - Molecular pathway analysis pipeline University of Michigan Applied Systems Biology Core Multi-scalar data analysis and integration, including cross-species comparison University of Michigan Applied Systems Biology Core Nephroseq - data extraction service University of Michigan Applied Systems Biology Core Protein data-mining workflow - Molecular pathway analysis pipeline University of Michigan Applied Systems Biology Core Protein data-mining workflow - proteomics data analysis pipeline University of Michigan Applied Systems Biology Core Quantitative morphometric analyses of kidney biopsy samples University of Michigan Applied Systems Biology Core TranSMART CProbe - data extraction service University of Michigan Applied Systems Biology Core TranSMART CureGN - data extraction service University of Michigan Applied Systems Biology Core TranSMART NEPTUNE- data extraction service University of Michigan Applied Systems Biology Core Vitessce - data extraction service University of Michigan Applied Systems Biology Core CELLxGENE - access/support University of Michigan Data Analytic Services Core Develop generalized workflow for integrative web-based analysis University of Michigan Data Analytic Services Core Investigating biomarker association (gene, protein, metabolite level) in clinical existing cohorts through TranSMART instance University of Michigan Data Analytic Services Core Nephroseq - access/support University of Michigan Data Analytic Services Core TranSMART CProbe - access/support University of Michigan Data Analytic Services Core TranSMART CureGN - access/support University of Michigan Data Analytic Services Core TranSMART NEPTUNE - access/support University of Michigan Data Analytic Services Core Vitessce - access/support University of Michigan Data Analytic Services Core Data analysis - cellular and whole animal physiological studies, or imaging studies University of Pittsburgh All Cores Bioinformatics and biostatistical support WashU Metabolism Core Stable isotope flux studies- proximal tubules: 15N-glutamine: data provisioning WashU Metabolism Core Stable isotope tracing studies in vivo: 13C-glucose: data provisioning WashU Metabolism Core Stable isotope tracing studies in vivo: 13C-glutamine: data provisioning WashU Metabolism Core Stable isotope tracing studies in vivo: 13C-palmitate and 13C-oleate: data provisioning WashU Metabolism Core -
Data Provisioning
Data transfer Indiana University Intravital core/Molecular Imaging Resource cores Dietary assessment services to investigate dietary patterns and biomarkers of dietary intake and food metabolism Johns Hopkins University Biomedical Resource Core (C-DSSL) Genomics dataset w/ deep phenotyping Johns Hopkins University Biomedical Resource Core (C-DSSL) Kidney Precision Medicine Center of Excellence (KPMCOE)—EMR registry Johns Hopkins University Biomedical Resource Core (C-DSSL) Large longitudinal cohort study data from racially and socioeconomically diverse populations Johns Hopkins University Biomedical Resource Core (C-DSSL) Metabolomics dataset w/ deep phenotyping Johns Hopkins University Biomedical Resource Core (C-DSSL) Proteomics dataset w/ deep phenotyping Johns Hopkins University Biomedical Resource Core (C-DSSL) Publicly accessible biospecimen repositories and datasets to support or conduct biomarker studies and secondary data analyses Johns Hopkins University Biomedical Resource Core (C-DSSL) Big data transformation & pipeline development: Tools for data collection to support clinical research UAB-UCSD Clinical Core Cloud-based multimodal databases for AKI and critical care nephrology research studies: Sepsis-AKI datasets UAB-UCSD Clinical Core Database development UAB-UCSD Clinical Core Clinical and molecular interactions in investigators’ data sets University of Michigan Applied Systems Biology Core Data provisioning University of Pittsburgh All Cores Stable isotope flux studies- proximal tubules: 15N-glutamine: data provisioning WashU Metabolism Core Stable isotope tracing studies in vivo: 13C-glucose: data provisioning WashU Metabolism Core Stable isotope tracing studies in vivo: 13C-glutamine: data provisioning WashU Metabolism Core Stable isotope tracing studies in vivo: 13C-palmitate and 13C-oleate: data provisioning WashU Metabolism Core -
Laboratory Services
Microbiome Johns Hopkins University Biomedical Resource Core (B-DSSL) Biomarker measurement - Clinical Chemistry Johns Hopkins University Biomedical Resource Core (C-DSSL) Biomarker measurement - Immunoassays Johns Hopkins University Biomedical Resource Core (C-DSSL) Biorepository support - Processing aliquoting, short- and long-term sample storage Johns Hopkins University Biomedical Resource Core (C-DSSL) Healthy volunteer samples for Reference Range Johns Hopkins University Biomedical Resource Core (C-DSSL) Polymer synthesis for making nanoparticles Johns Hopkins University Biomedical Resource Core (C-DSSL) Prospective remnant sample collection Johns Hopkins University Biomedical Resource Core (C-DSSL) Stored biospecimen samples from completed studies Johns Hopkins University Biomedical Resource Core (C-DSSL) Fluorophore conjugation with DSPE-PEG NU-USC Biomedical Resource Core In vitro cell viability evaluation - MTS assay/plate reader NU-USC Biomedical Resource Core In Vitro Micelles Binding Evaluation NU-USC Biomedical Resource Core In Vitro Micelles Binding Evaluation: Confocal Microscopy NU-USC Biomedical Resource Core In Vitro Micelles Binding Evaluation: Flow Cytrometry NU-USC Biomedical Resource Core In Vitro Micelles Efficacy Evaluation NU-USC Biomedical Resource Core In Vitro Micelles Efficacy: Quantification of markers related - qPCR NU-USC Biomedical Resource Core In Vitro Micelles Efficacy: Quantification of proteins related - ELISA NU-USC Biomedical Resource Core In Vitro Micelles Efficacy: Quantification of proteins related - Western blot NU-USC Biomedical Resource Core In vitro studies of micelles with Collecting Duct cells - Cortical collecting duct (M1) NU-USC Biomedical Resource Core In vitro studies of micelles with Collecting Duct cells - Cortical collecting duct (Principal cells) NU-USC Biomedical Resource Core In vitro studies of micelles with Collecting Duct cells - Inner Medullary NU-USC Biomedical Resource Core In vitro studies of micelles with Proximal Tubule cells NU-USC Biomedical Resource Core In Vivo Micelles Therapeutic Efficacy: Immunohistochemistry (IHC) Imaging NU-USC Biomedical Resource Core In Vivo Micelles Therapeutic Efficacy: using Rapid Model NU-USC Biomedical Resource Core Incorporation of conjugated siRNA into micelles NU-USC Biomedical Resource Core Micelles formation NU-USC Biomedical Resource Core Nanocarrier/micelles characterization: Morphology - Transmission electron microscopy (TEM) NU-USC Biomedical Resource Core Nanocarrier/micelles characterization: particles size - Dynamic Light Scattering (DLS) NU-USC Biomedical Resource Core Nanocarrier/micelles characterization: Polydispersity Index (PDI)- Dynamic Light Scattering (DLS) NU-USC Biomedical Resource Core Nanocarrier/micelles characterization: RNA incorporation - Gel Electrophoresis NU-USC Biomedical Resource Core Nanocarrier/micelles characterization: RNA protection against nucleases - Gel Electrophoresis NU-USC Biomedical Resource Core Nanocarrier/micelles characterization: zeta potential - Dynamic Light Scattering (DLS) NU-USC Biomedical Resource Core Peptide purification NU-USC Biomedical Resource Core Peptide purification: High-Performance Liquid Chromatography (HPLC) NU-USC Biomedical Resource Core Peptide purification: Matrix-Assisted Laser Desorption/Ionization (MALDI) NU-USC Biomedical Resource Core Purified peptide conjugation with DSPE-PEG for micelles synthesis NU-USC Biomedical Resource Core Purified peptide conjugation with DSPE-PEG purification: High-Performance Liquid Chromoatography (HPLC) NU-USC Biomedical Resource Core Purified peptide conjugation with DSPE-PEG purification: Matrix-Assisted Laser Desorption/Ionization (MALDI) NU-USC Biomedical Resource Core Quantification of drug encapsulation in nanocarriers by HPLC NU-USC Biomedical Resource Core siRNA conjugation with DSPE-PEG NU-USC Biomedical Resource Core Applications and use of magnetic ranking cytometry (LEAPFROG Platform) NU-USC Resource Development Core Cell surfaceome library lentiviral prep NU-USC Resource Development Core Cell surfaceome library plasmid prep NU-USC Resource Development Core Use of microfluidc chips for cell sorting (LEAPFROG Platform) NU-USC Resource Development Core AKI Biological Sample Repository UAB-UCSD Clinical Core Bulk RNA seq - from Fastq to analyses UAB-UCSD Pre-Clinical Core Bulk RNA seq - sample to analyses UAB-UCSD Pre-Clinical Core LC-MS/MS Creatinine determination (per test) UAB-UCSD Pre-Clinical Core Use of a microsurgical workstation (per hour) UAB-UCSD Pre-Clinical Core Structured RNA-DNA sequence data integration University of Michigan Applied Systems Biology Core Functional imaging analyses (e.g., Ca2+ imaging) University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core HPLC-Fl - ATP Metabolome University of Pittsburgh Model Systems Core Purine Metabolome by UPLC-MS/MS University of Pittsburgh Model Systems Core Epithelial transport in Ussing chambers University of Pittsburgh Physiology Core Functional imaging analyses (e.g., Ca2+ imaging) University of Pittsburgh Physiology Core In vitro microperfusion of isolated tubules for functional fluorescence assays of single cell function University of Pittsburgh Physiology Core In vitro microperfusion of isolated tubules for measurement of transepithelial ion and solute transport University of Pittsburgh Physiology Core Isolation of single nephron segments for immunofluorescence, enzyme assays, RNA and protein isolation University of Pittsburgh Physiology Core Isolation of Xenopus laevis oocytes University of Pittsburgh Physiology Core Oocyte two-electrode voltage clamp University of Pittsburgh Physiology Core Patch-clamp analyses University of Pittsburgh Physiology Core Quantification of surface protein expression University of Pittsburgh Physiology Core BCA Assay for normalization of fatty acid oxidation data WashU Metabolism Core Branched chain amino acid oxidation in tissue ex vivo using 14C-KIVA WashU Metabolism Core Cell quantification with Biotek Lionheart (to normalize Seahorse data) WashU Metabolism Core Fatty acid oxidation in tissue ex vivo using 3H-palmitate WashU Metabolism Core Glucose oxidation in tissue ex vivo using 14C-pyruvate WashU Metabolism Core Placement of jugular catheter for administration of stable isotopes WashU Metabolism Core Seahorse bioflux analyzer (XF24/XF96) to measure glucose oxidation in primary proximal tubule cells WashU Metabolism Core Seahorse bioflux analyzer (XF24/XF96) to measure glutamine oxidation in primary proximal tubule cells WashU Metabolism Core Seahorse bioflux analyzer (XF24/XF96) to measure glycolysis (i.e. extracellular acidification rate) in primary proximal tubule cells WashU Metabolism Core Seahorse bioflux analyzer (XF24/XF96) to measure mitochondrial oxidative respiration in primary proximal tubule cells WashU Metabolism Core Seahorse bioflux analyzer (XF24/XF96) to measure palmitate (fatty acid) oxidation in primary proximal tubule cells WashU Metabolism Core Stable isotope flux studies- proximal tubules: 13C-glucose WashU Metabolism Core Stable isotope flux studies- proximal tubules: 13C-glutamine WashU Metabolism Core Stable isotope flux studies- proximal tubules: 13C-palmitate WashU Metabolism Core Stable isotope tracing studies in vivo: 13C-glucose WashU Metabolism Core Stable isotope tracing studies in vivo: 13C-glutamine WashU Metabolism Core Stable isotope tracing studies in vivo: 13C-palmitate and 13C-oleate WashU Metabolism Core Stable isotope tracing studies in vivo: 15N-glutamine WashU Metabolism Core Stable isotope tracing studies in vivo: branched chain amino acids WashU Metabolism Core Untargeted metabolomics - lipids WashU Metabolism Core Untargeted metabolomics - water soluble WashU Metabolism Core Analysis of variant protein trafficking in cultured cells WashU Variant Validation Core Analysis of variant UMOD protein trafficking in cultured cells WashU Variant Validation Core Analysis of VUS in non-COL4A genes through design and implementation of tailored laboratory assays WashU Variant Validation Core COL4A3 intronic VUS analysis by minigene RNA splicing assays using transfected cells WashU Variant Validation Core COL4A3 VUS (missense) analysis by N-terminal split nano-Luciferase collagen IV assembly and secretion assays in transfected cells WashU Variant Validation Core COL4A3 VUS (missense) analysis by split C-terminal nano-Luciferase collagen IV assembly and secretion assays using transfected cells WashU Variant Validation Core COL4A3 VUS analysis by high resolution quantitative immunofluorescence imaging in paraffin sections of kidney biopsies WashU Variant Validation Core COL4A4 intronic VUS analysis by minigene RNA splicing assays using transfected cells WashU Variant Validation Core COL4A4 VUS (missense) analysis by N-terminal split nano-Luciferase collagen IV assembly and secretion assays in transfected cells WashU Variant Validation Core COL4A4 VUS (missense) analysis by split C-terminal nano-Luciferase collagen IV assembly and secretion assays using transfected cells WashU Variant Validation Core COL4A4 VUS analysis by high resolution quantitative immunofluorescence imaging in paraffin sections of kidney biopsies WashU Variant Validation Core COL4A5 intronic VUS analysis by minigene RNA splicing assays using transfected cells WashU Variant Validation Core COL4A5 VUS (missense) analysis by N-terminal split nano-Luciferase collagen IV assembly and secretion assays in transfected cells WashU Variant Validation Core COL4A5 VUS (missense) analysis by split C-terminal nano-Luciferase collagen IV assembly and secretion assays using transfected cells WashU Variant Validation Core COL4A5 VUS analysis by high resolution quantitative immunofluorescence imaging in paraffin sections of kidney biopsies WashU Variant Validation Core Intronic non-COL4A gene VUS analysis by minigene RNA splicing assays using transfected cells WashU Variant Validation Core -
Methods Development
Methods development in microscopy and molecular imaging Indiana University Intravital core/Molecular Imaging Resource cores Cell surface target-specific phenotypic screening NU-USC Resource Development Core Cell surfaceome target detection optimization and characterization (LEAPFROG Platform) NU-USC Resource Development Core Injection moulding based microfluidic chip fabriacation (LEAPFROG Platform) NU-USC Resource Development Core Target-antibody-magnetic nanoparticles coupling/optimization NU-USC Resource Development Core Design of epidemiological, clinical studies or clinical trials UAB-UCSD Clinical Core Forms, manual of operations, and/or instrument development UAB-UCSD Clinical Core Research Resource Development (https://www.uab.edu/medicine/obriencenter/cores/development-core) UAB-UCSD Resource Development Core General data result interpretation and discussion, development of next steps University of Michigan Applied Systems Biology Core General troubleshooting University of Michigan Applied Systems Biology Core Initial study design consultation University of Michigan Applied Systems Biology Core Metabolomics driven analysis workflow University of Michigan Applied Systems Biology Core Spatial metabolomics service (sample process and data analysis) University of Michigan Applied Systems Biology Core Transcript driven data-mining workflow - Bulk RNA Sequencing analysis pipeline University of Michigan Applied Systems Biology Core Transcript driven data-mining workflow - Single cell/single nuc RNA Sequencing analysis pipeline University of Michigan Applied Systems Biology Core Transcript driven data-mining workflow - Streamlined self-organizing map (SOM) to identify functional subgroups University of Michigan Applied Systems Biology Core Transcript driven data-mining workflow - Weighted Correlation Network Analysis (WGCNA) to identify co-expressed molecular elements within datasets University of Michigan Applied Systems Biology Core Design of assays for other protein trafficking in cultured cells WashU Variant Validation Core -
Microscopy/Imaging Services
Characterization of transgenic rodents expressing fluorescently tagged proteins in the kidney Indiana University Intravital Microscopy Resource Core Fluorescence lifetime imaging of endogenous and exogenous fluorophores in the kidney Indiana University Intravital Microscopy Resource Core Intravital Imaging: Apoptosis and necrosis Indiana University Intravital Microscopy Resource Core Intravital Imaging: Cellular oxidative stress Indiana University Intravital Microscopy Resource Core Intravital Imaging: Characterization of in vivo fluorescent probe delivery to the kidney Indiana University Intravital Microscopy Resource Core Intravital Imaging: Glomerular Permeability Indiana University Intravital Microscopy Resource Core Intravital Imaging: Microvascular flow Indiana University Intravital Microscopy Resource Core Intravital Imaging: Microvascular permeability Indiana University Intravital Microscopy Resource Core Intravital Imaging: Mitochondrial function Indiana University Intravital Microscopy Resource Core Intravital Imaging: Proximal tubule endocytosis Indiana University Intravital Microscopy Resource Core 3-dimensional confocal tissue cytometry of kidney tissue Indiana University Molecular Imaging Resource Core CODEX multiplexed cytometry of mouse and human kidney tissue, other tissues/organs Indiana University Molecular Imaging Resource Core In situ sequencing of mouse and human kidney tissue (Xenium) Indiana University Molecular Imaging Resource Core Lightsheet microscopy Indiana University Molecular Imaging Resource core Spatial Transcriptomics of mouse and human kidney tissue (Visium SD, Visium FFPE) Indiana University Molecular Imaging Resource Core Images w/ deep phenotyping Johns Hopkins University Biomedical Resource Core (C-DSSL) Functional renal imaging (tracer dependent, per hour) UAB-UCSD Pre-Clinical Core Image Analysis UAB-UCSD Pre-Clinical Core Nuclear Imaging (3D) UAB-UCSD Pre-Clinical Core Nuclear imaging (Gamma camera, SPECT/CT, PET/CT) (per hour) UAB-UCSD Pre-Clinical Core Optical Imaging (Bioluminescence, Fluorescence) (per hour) UAB-UCSD Pre-Clinical Core Structural and metabolic imaging (preclinical MRI- BOLD) UAB-UCSD Pre-Clinical Core Structural and metabolic imaging (Pulse Wave Velocity Imaging) UAB-UCSD Pre-Clinical Core Structural and metabolic imaging (US, MRI, microCT) (per hour) UAB-UCSD Pre-Clinical Core Histopathology University of Pittsburgh All Cores CLEM imaging of kidneys University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Confocal microscopy - Laser scanning confocal microscopy University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Confocal microscopy - Spinning disk confocal microscopy University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Confocal microscropy - Fluorescent lifetime imaging University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Confocal microscropy - Fluorescent recovery after photobleaching University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Confocal microscropy - Ribbon scanning confocal microscopy for cleared organs/tissues University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Electron Microscopy - CLEM University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Electron Microscopy - Freeze fracture microscopy University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Electron Microscopy - Freeze substitution University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Electron Microscopy - Immuno-Electron microscopy University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Electron Microscopy - Negative staining University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Electron Microscopy - Platinum replica electron microscopy University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Electron Microscopy - Scanning electron microscopy (field-emission) University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Electron Microscopy - Transmission electron microscopy University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Electron Microscopy - Ultramicrotomy University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Electron Microscopy - Ultrathin cryo EM University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Image Analysis - Imaris University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Image Analysis - Leica LASX University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Image Analysis - Metamorph University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Image Analysis - NIH image/FIJI University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Image Analysis - NIS elements University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Image Analysis - Photoshop University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core iPOL imaging University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Live-cell microscopy - Fluorescent lifetime imaging University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Live-cell microscopy - Fluorescent recovery after photobleaching University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Live-cell microscopy - Incubator microscopy University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Live-cell microscopy - Lattice light sheet microscopy University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Live-cell microscopy - Spinning disk confocal microscopy University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Live-cell microscopy -Microinjection University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Meso-Spim light sheet microscopy University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Multiphoton microscopy - Fluorescent lifetime imaging University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Multiphoton microscopy - Fluorescent recovery after photobleaching University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Multiphoton microscopy - Intravital imaging University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Multiphoton microscopy - Multiphoton confocal microscopy University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core SEM imaging of fractured kidneys University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Standard light microscopy - Brightfield, darkfield, epifluorescence, DIC University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Standard light microscopy - Macro (stereo) imaging microscopy University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Super-resolution microscopy - AX/NSPARC University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Super-resolution microscopy - CREST University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Super-resolution microscopy - STED University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Super-resolution microscopy - STORM University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core TRIF Microscopy - TIRF imaging acquisition and analysis University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Whole slide scanning - brightfield and epifluorescence University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core -
Project Consultation
AKI study design and planning for imaging studies Indiana University Intravital core/Molecular Imaging Resource cores CKD study design and planning for imaging studies Indiana University Intravital core/Molecular Imaging Resource cores Project consultation for imaging studies Indiana University Intravital core/Molecular Imaging Resource cores Initial project consultation to select appropriate Basic Science Dietary and Social Stressor Laboratory resources Johns Hopkins University Biomedical Resource Core (B-DSSL) Study design, Basic Science Dietary and Social Stressor Laboratory Johns Hopkins University Biomedical Resource Core (B-DSSL) Consultation on design and features of translational studies in the community Johns Hopkins University Biomedical Resource Core (C-DSSL) Initial project consultation to select appropriate Clinical Science Dietary and Social Stressor Laboratory resources Johns Hopkins University Biomedical Resource Core (C-DSSL) Study design consultation and data and biobanked specimens from studies on behavioral interventions for lifestyle changes Johns Hopkins University Biomedical Resource Core (C-DSSL) Study design, Clinical Science Dietary and Social Stressor Laboratory Johns Hopkins University Biomedical Resource Core (C-DSSL) Applications of immunomagnetic cell sorting (LEAPFROG Platform) NU-USC Biomedical Resource Core Designing in vitro studies NU-USC Biomedical Resource Core Designing in vivo studies NU-USC Biomedical Resource Core Feasibility assessment NU-USC Biomedical Resource Core Identifying pathway for therapy NU-USC Biomedical Resource Core Identifying targeting peptides NU-USC Biomedical Resource Core In Vivo Micelles Therapeutic Efficacy : Hematoxylin and Eosin (H&E) Imaging NU-USC Biomedical Resource Core In Vivo Therapeutic Efficacy: NU-USC Biomedical Resource Core In Vivo Therapeutic Efficacy: Guidance NU-USC Biomedical Resource Core NW Background search NU-USC Biomedical Resource Core NW Grant proposal assistance NU-USC Biomedical Resource Core Cell-type specific antigen/target selection for magnetic ranking cytometry NU-USC Resource Development Core Pooled CRISPR editing and phenotypic screening experimental designs NU-USC Resource Development Core Rare-cell isolation/enrichment using the LEAPFROG Platform NU-USC Resource Development Core Use of Cell Surfaceome lentiviral CRISPR gRNA library NU-USC Resource Development Core AKI Clinical Study Initiation and Conduct UAB-UCSD Clinical Core AKI Epidemiological Study Initiation and Conduct UAB-UCSD Clinical Core AKI Study Planning and Design UAB-UCSD Clinical Core Data Safety and Monitoring UAB-UCSD Clinical Core Bulk RNA seq UAB-UCSD Pre-Clinical Core Shared Data Mining Services - Initial study design consultation University of Michigan Applied Systems Biology Core Consultation for development of new approaches to study the kidney and lower urinary tract University of Pittsburgh All Cores Choosing the right metabolic assay WashU Metabolism Core High resolution respirometry (Oroboros) WashU Metabolism Core Metabolomics and stable isotope flux study- Zoom discussion with Patti lab over experimental design WashU Metabolism Core Choosing an assay for COL4A3 VUS analysis WashU Variant Validation Core Choosing an assay for COL4A4 VUS analysis WashU Variant Validation Core Choosing an assay for COL4A5 VUS analysis WashU Variant Validation Core Choosing an assay for non-COL4A gene VUS analysis WashU Variant Validation Core -
Publication Support
Grant Assistance Indiana University Intravital core/Molecular Imaging Resource cores Manuscript development/publication support Indiana University Intravital core/Molecular Imaging Resource cores Hopkins Manuscript development Johns Hopkins University Biomedical Resources Core NW Manuscript assistance NU-USC Biomedical Resource Core NW Publication Assistance NU-USC Biomedical Resource Core Assistance with manuscript development or publication support UAB-UCSD All Cores Conference, meeting abstract preparation University of Michigan All cores Conference, meeting presentation support University of Michigan All cores Grant support - LOS University of Michigan All cores Grant support - Writing University of Michigan All cores Michigan Manuscript development University of Michigan All cores Manuscript development University of Pittsburgh All Cores Assistance with manuscript development or publication support WashU Metabolism Core -
Training/Development
Training- Includes Bioinformatics and Digital Image Analysis Indiana University Intravital core/Molecular Imaging Resource cores Training in Intravital microscopy Indiana University Intravital Microscopy Resource Core Isolated Nephron segment Dissection Johns Hopkins University Biomedical Resource Core (B-DSSL) Kidney Slice Preparation Johns Hopkins University Biomedical Resource Core (B-DSSL) Use of injection moulded microfluidic chips for cell sorting (LEAPFROG platform) NU-USC Resource Development Core Bulk RNA seq training (per day) UAB-UCSD Pre-Clinical Core Training (per hour/per day) UAB-UCSD Pre-Clinical Core CellxGENE training University of Michigan Applied Systems Biology Core General bioinformatic tool training (eg. R) University of Michigan Applied Systems Biology Core Nephroseq training University of Michigan Applied Systems Biology Core Transcript driven data analysis - Bulk RNA sequencing analysis pipeline University of Michigan Applied Systems Biology Core Transcript driven data analysis - Molecular pathway analysis pipeline University of Michigan Applied Systems Biology Core TranSMART CProbe training University of Michigan Applied Systems Biology Core TranSMART CureGN training University of Michigan Applied Systems Biology Core TranSMART NEPTUNE training University of Michigan Applied Systems Biology Core Vitessce training University of Michigan Applied Systems Biology Core Training in live-cell and intravital approaches to study the biology/pathobiology of kidney and bladder tissues University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Training in microscope/equipment usage University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Training in quantitative image analysis University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Training in sample preparation of kidney and bladder tissues for light and electron microscopic analysis University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Training in specialized sample preparation to perform labeling and analysis of cleared organs and tissues University of Pittsburgh Kidney Imaging: Developing Novel and Innovative Tools (KIDNIT) Development Core Nephron segment microdissection/isolation and microperfusion training University of Pittsburgh Physiology Core Patch-clamp training University of Pittsburgh Physiology Core Training on use of microinjectors University of Pittsburgh Physiology Core Training on use of micropipette pullers and microforges to craft micropipettes for patch-clamp and in vitro microperfusion University of Pittsburgh Physiology Core Two-electrode voltage clamp training University of Pittsburgh Physiology Core Xenopus laevis technologies training University of Pittsburgh Physiology Core Training in the performance of collagen IV heterotrimerization assays using split nanlLuciferase tagged COL4A chains WashU Variant Validation Core