Research Cores/Services Provided
About
The PCEN at the University of Virginia supports three biomedical research cores to assist PCEN investigators: the Single Cell Epigenomics, Transcriptomics and Bioinformatics Core; the Histology Core; and the Physiology Core. Together, these cores provide state-of-the-art services in epigenomics, transcriptomics, spatial transcriptomics, bioinformatics, histology, and physiology to the two main research projects, PCEN Pilot Projects, and independently funded pediatric kidney researchers at UVA and other institutions. The scope of the cores is in line with the overall theme of this PCEN: “Kidney Development and Disease: Cell Fate and Precursors of Disease in the Young and Adult.”
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Aim 1: To provide support and services for transcriptome and epigenome studies, validation, and functional/phenotypic analysis.
Aim 2: To support PCEN ‘omics data analysis with state-of-the-art bioinformatics approaches.
Research and Educational Resources provided by the Core
• scRNA-seq and scATAC-seq (10X Genomics Chromium and Fluidigm C1 systems).
• scMultiome ATAC-seq+gene expression (10X Genomics Chromium).
• Spatial transcriptomics (10X Genomics Visium and Visium HD).
• Bulk RNA-seq and bulk ATAC-seq.
• ChIP-seq, CUT&Tag and CUT&RUN.
• ‘omics data analysis with state-of-the-art bioinformatics approaches services.
• Validation of RNA-seq data (qPCR, ISH, RNAScope).
• Functional studies using CRISPR/Cas for gene editing.
• Development of new protocols & bioinformatic tools
• Training and Education.
• Project Consultation: design and analysis.
• Support for the preparation of grant applications and manuscripts.
• Access to state-of-the-art equipment and computational resources.
Contact Investigators:
Silvia Medrano Ph.D., Co-Director
Senior Research Scientist
University of Virginia, CHRC, Department of Pediatrics
Email: sm8z@virginia.edu
Nathan Sheffield Ph.D., Co-Director
Associate Professor, School of Medicine, University of Virginia
Email: ns5bc@virginia.edu
Jason P. Smith Ph.D.
Bioinformatician University of Virginia, CHRC,
Department of Pediatrics
Email: jps3dp@virginia.edu
Histology Core
Director: Silvia Medrano, Ph.D. (sm8z@virginia.edu)
Contact: Maria Luisa S. Sequeira-Lopez, M.D. (msl7u@virginia.edu)
Services: – Immunostaining and immunohistochemistry (IHC) – Histological staining (H&E, PAS, and others) – Frozen tissue sectioning – Tissue processing and harvesting – Fluorescent reporter visualization – Antibody and reagent provision – Microscopy and morphological analysis – Experimental design consultation
Physiology Core
Director: Silvia Medrano, Ph.D. (sm8z@virginia.edu)
Contact: Maria Luisa S. Sequeira-Lopez, M.D. (msl7u@virginia.edu)
Services: – Blood pressure measurements – Glomerular filtration rate (GFR) measurements – Metabolic cage studies – Renin ELISA and plasma renin measurements – Surgical procedures – Experimental design consultation