Facilities and Resources description for grants


Flow Cytometry Instrumentation and High Performance Analytical Pipelines. The Unified Flow Cytometry Core is the centralized FACS facility for the University of Pittsburgh School of Medicine. The core houses twelve high-speed instruments under the auspices of a highly experienced Core Director, Dr. Lisa Borghesi, PhD. Equipment includes three sorters and nine analyzers, two of which are state-of-the art high-dimensional 64 channel cytometers. In addition to the standard blue, red and violet lines, instruments are configured with green, yellow-green and/or UV lasers. The sorters are: a biocontained BD Aria IIU (5 laser, 17 detector), biocontained BD Aria II (5 laser, 17 detector), and non-contained BD Aria IIU (3 laser, 12 detector). The flow analyzers are: BD LSRFortessa (5 laser, 18 detector), BD LSRFortessa (4 laser, 15 detector), BD LSRFortessa (4 laser, 15 detector), BD LSRII (5 laser, 17 detector), BD LSRII (5 laser, 17 detector), two Cytek Aurora spectral instruments (5 laser, 64 channel), Attune NxT (4 laser, 16 detector) and Amnis ImageStream imaging cytometer (6 laser, 10 detector). Biocontained sorters and analyzers support BSL2+ research.

Integrated analytical pipelines include algorithmic clustering (viSNE, SPADE, FlowSOM, PCA, K-means, etc.) in a high-performance environment, novel algorithm development/application, and next-gen sequencing:

· Center for Research Computing - algorithmic analysis. Two high-performance clusters enable computational flow cytometry analyses to be carried out independently and simultaneously on individual sets of processors: H2P (29-core Broadwell processor comprised of 96 nodes, 64 GB RAM, and 256 BD SSD) and HTC (16-core Haswell processors comprised of 20 nodes, 256 GB RAM, and 256 BD SSD).

· Center for Causal Discovery - development and application of novel computational algorithms. Integrates biomedical and data scientists to develop and advance new constraint-based and Bayesian algorithms in a supercomputing environment. The CCD is a joint effort of approximately 40 investigators at Pitt, Carnegie Mellon University, the Pittsburgh Supercomputing Center, and Yale University.

· Health Sciences Next Generation Sequencing Core - bulk and single cell sequencing. Supports high-throughput DNA and RNA sequencing. Equipment includes the 10X Genomics Chromium platform, Illumina NovaSeq 6000 series high throughput sequencers and NextSeq500 sequencers. The associated Genome Analysis Core provides data analysis services.

· University of Pittsburgh Center for Systems Immunology. Interfaces with systems biology in all of its forms. This collaborative platform is overseen by Center Director Harinder Singh, PhD, an international expert in the molecular underpinnings of lymphocyte development and immune responses. The mission of the Center is to harness newly emerging experimental, computational and engineering approaches to analyze the immune system in health and disease, thereby facilitating its rational therapeutic manipulation. Investigators collaborate longitudinally to work on major problems of translational interest relevant to human immunological disease.