Directory of Laboratory and Computing Research Resources
Preclinical Phenotyping Core (PPC)
The Preclinical Phenotyping Core (PPC) provides access to behavioral testing equipment for rats and mice, and phenotyping expertise encompassing domains of cognition, anxiety, depression, general exploratory and locomotor activity, nociception, social behavior, and aging.
Innovative Technologies Development (ITD) Core
The Innovative Technologies Development (ITD) Core provides cutting edge gene targeting strategies using various methods, including CRISPR-Cas9 gene targeting.
Genetic Engineering in mice using CRISPR/Cas9 technology:
Dr. Sebastien Gingras will consult with the investigator on the design of the targeting strategy. Detailed analysis of the gene structure then provides the best targeting strategy to meet the investigator’s objectives. We provide complete a turnkey service that includes project design, synthesis of sgRNA and Cas9 mRNA, assessment of reagents quality, editing efficiency, and mouse genotyping.
Classical transgenesis: Design of transgenic vectors.
Assistance with gene editing in cell lines using CRISPR: We offer designs and can provide assistance for genome engineering projects in cell lines. We will advise the investigator on the most effective method to generate their desired cell lines. We will provide the design for a custom targeting strategy, identify targets sites, the design of targeting vectors, cloning procedure, and genotyping strategy.
Other/New: The Innovative Technologies Development Core will also consider developing new emerging technologies or other services that would be valuable to investigators of the University of Pittsburgh.
Genomics Analysis Core
The Genomics Analysis Core (GAC) provides bioinformatics analysis for data from all genomics platforms including microarrays and next generation sequencing applications. The GAC provides support for all aspects of translational studies – from experimental design to data analysis to publication. The GAC works closely with the Health Science Library System Mol Bio Service (HSLS – Mol Bio), the Center for Research Computing, in directing researchers appropriate resource for genomics education, analysis and computing.
Bioinformatic Data Analysis
The GAC provides bioinformatics support for RNA Seq, Exome Seq, Whole Genome Seq, ChiP Seq, ATAC Seq and other emerging genomic applications.
High Throughput Computing
The GAC works with the Center for Research Computing (CRC) and the Pittsburgh Supercomputing Center (PSC) in development and implementation of bioinformatic pipelines and High Performance Computing (HPC) resources.
Health Record Research Request (R3)
R3 is a service of the Department of Biomedical Informatics (DBMI), provisioning UPMC clinical data and authorizing additional UPMC data sources for research.
Health Record Research Request (R3) is a service of the Department of Biomedical Informatics (DBMI) managed by the Chief Research Informatics Officer (CRIO), sponsored in part by the Clinical and Translational Sciences Institute and Institute for Precision Medicine. Pitt and UPMC desire to make clinical data available for research. Under the CRIO, on behalf of UPMC, DBMI staff provision data for research (in some cases as Honest Brokers). R3 is this service or process of provisioning UPMC clinical data and of authorizing additional UPMC data sources for research. R3 is available for use by researchers of the University of Pittsburgh, and for UPMC projects requiring research datasets. To engage R3 please use the R3 Intake Form (less than 30 seconds to fill out including principal investigator contact information and pasting in a brief project description). R3 team can be contacted with any questions at HealthR3@pitt.edu.
Single Cell Core
The Single Cell Core performs cutting edge assays in single cell technologies using the 10X Genomics Chromium platform to facilitate university researchers projects. Services include: 3’ and 5’ Gene Expression assays, TCR and BCR coupled with gene expression, Single Cell ATAC seq, CITE Seq cell surface protein expression coupled with mRNA gene expression, and Perturb Seq is expected to be available winter 2019. The Single Cell Core also performs experimental design consultations and data analysis.
The Committee for Oversight of Research and Clinical Training Involving Decedents (CORID)
CORID is administrated by the Office for Oversight of Anatomic Specimens (OOAS) and is responsible for the review and approval of all research and educational/clinical training activities that require the use of human cadaveric tissue and decedent medical records.
All human biological materials collected for research purposes and stored in a biorepository must be registered in accordance with the Tissue Policy and the repository must be registered for a transfer request (MTA) to be approved.
Health Sciences Metabolomics and Lipidomics Core (HSMLC)
Welcome to the Health Sciences Metabolomics and Lipidomics Core (HSMLC)
The Health Sciences Metabolomics and Lipidomics Core (HSMLC) is a Health Sciences Core Research Facility (HSCRF) located in the Department of Pharmacology & Chemical Biology. We provide assistance with projects that range in size from isolated experiments to major collaborations involving global analyses related to metabolites and lipids, and metabolic flux studies. We have working relationships with C3M, CMM and the Small Molecule Biomarker Core in order to facilitate highly collaborative research involving endocrinology and metabolism, the microbiome and quantitative biomarker analysis.
Our goal is provide the best assistance we can, beginning with the experimental design in order to provide you with the optimum data for your project. Ideally it is best to contact us before planning an experiment so we can assist with various parameters including numbers per group, sample storage and processing. However, many investigators have samples already stored from an ongoing study. In this event we can define realistic expectations of data output based on the sample condition and previous processing.
Please vist our web site or contact us for more information.
Resources for Next Generation Sequencing (NGS)
The Health Sciences Next Generation Sequencing Working Group has developed a guide to help Pitt investigators find local resources for designing experiments, sequencing samples, analyzing data, and storing data for research involving Next Generation Sequencing (NGS). There is a quick reference card for the experienced user who knows what he or she needs, a self-guided tour through the available resources for those who are less experienced, and a direct contact for those who want individualized guidance. (Keywords: statistics, software, illumina, ion, pgm, proton, nextseq, miseq, novaseq, genome, RNA, DNA, compute, computing, data, storage)
Pitt Gnotobiotic Facility
The Pitt Gnotobiotic facility is a fee-for-service core that allows for experiments requiring germ-free (without bacteria, fungi and exogenous viruses) and gnotobiotic (‘known microbiota’) mice. The facility allows for the use of commercially available strains of mice in addition to a limited selection of ‘knockout’ mice. Use of the facility is determined on a first come/first served basis, but the committee on gnotobiotics reserves the right to limit the size and scope of experiments to allow for multiple users. Assistance in gavaging or otherwise associating mice with microbiota is possible. Tim Hand is willing to discuss experiment design and specifics to help ensure project success.
Available strains: C57BL/6, Balb/c
Soon: Rag1-/- on C57Bl/6 background
Office of Research Computing
The Office of Research Computing includes:
The Center for Research Computing (CRC) - https://crc.pitt.edu/resources
Pittsburgh Supercomputing Center (PSC) - http://www.psc.edu
Center for Research Computing
The mission of the CRC is to increase the impact and productivity of Pitt researchers through the use of advanced computing. We fulfill this mission by
- providing our community access to cutting-edge computer hardware and software for enabling transformative research,
- providing our community training workshops to educate users how to utilize the computing resources effectively,
- providing extended personalized consultation for improving researchers’ computational workflow and code performance through selection of better algorithms, parallelization techniques, improved use of input-output strategies, etc. We can also assist in grant proposals, justifying the requested computational hardware or personnel support.
An overview of CRC resources can be found at https://crc.pitt.edu/documentation/overview-to-crc-resources/
Hardware computing resources include SMP, GPU, MPI_OPA, and MPI_IB clusters and a High Throughput Computing (HTC) cluster designed for Health Sciences Research. Multiple data storage options are available, each consisting of hundreds of terabytes.
Pittsburgh Supercomputing Center
Pittsburgh Supercomputing Center is a joint effort of Carnegie Mellon University and the University of Pittsburgh. Established in 1986, PSC is supported by several federal agencies, the Commonwealth of Pennsylvania and private industry and is a leading partner in XSEDE (Extreme Science and Engineering Discovery Environment), the National Science Foundation cyberinfrastructure program.
PSC provides university, government and industrial researchers with access to several of the most powerful systems for high-performance computing, communications and data storage available to scientists and engineers nationwide for unclassified research. PSC advances the state of the art in high-performance computing, communications and data analytics and offers a flexible environment for solving the largest and most challenging problems in computational science.