The PCEN at the University of Virginia supports one biomedical research core to assist PCEN investigators in two important areas: 1) Transcriptome and epigenome technologies and 2) Bioinformatics. The Single Cell Epigenomics, Transcriptomics, and Bioinformatics Core is directed by two experienced researchers and staffed with highly trained personnel. The scope of the core is in line with the overall theme of this PCEN which is “Kidney Development and Disease: Cell Fate and Precursors of Disease in the Young and Adult.” The experimental approaches of the PCEN involve the examination of epigenetic mechanisms that control cell fate, plasticity, and identity and the cellular signals underlying the phenotypic transformation that occurs during kidney injury and repair.
The objective of the Core is to support the scientific goals of the PCEN by providing state-of-the-art services in the areas of epigenomics, transcriptomics, and bioinformatics to the two main research projects, PCEN Pilot Projects and independently funded pediatric kidney researchers at UVA and other institutions.
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 scATC-seq (10X Genomics Chromium and Fluidigm C1 systems).
• scMultiome ATAC-seq+gene expression (10X Genomics Chromium).
• 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.
Silvia Medrano Ph.D., Co-Director
Senior Research Scientist
University of Virginia, CHRC, Department of Pediatrics
Nathan Sheffield Ph.D., Co-Director