The Qualitative Research Core (QCR) supports all Children‘s Hospital of Philadelphia Research Institute personnel and faculty who are interested in utilizing qualitative methods. We support research teams with a wide range of qualitative research experience, including those who are new to qualitative research and those with established qualitative research portfolios. We are experienced in providing research support across a broad range of settings, including in-hospital clinical research, primary care, public health, and community-based settings. Our services are designed to support a wide range of needs, including free introductory videos, yearly seminars, customized project workshops, and hands-on project support and grantmaking.

The CHOP Microbiome Center is the sequencing and analytical resource of the PennCHOP Microbiome Program, providing end-to-end solutions for microbiome research. Our sequencing lab offers expertise in next-generation DNA sequencing for microbiome studies, working with customers to provide optimized workflows and protocols customized for each study. Our analytical lab provides expertise in bioinformatics and statistical analysis of microbiome data. We develop an analytical plan specific to your project and can integrate microbiome data with other data sources, such as metabolomics or dietary intake information.

Established in 2012, the CAG Sequencing Laboratory is fully equipped with state-of-art technology and experienced staff members. Sequencing operations are integrated with our Biorepository and Bioinformatics teams to keep all stages of a collaborator’s studies connected. The CAG sequencing lab offers cutting edge technologies in the Genomics field: NovaSeq, Single Cell 10xGenomics, various library preparations including bulk RNAseq, Whole Genome/Whole Exome, and Sanger Sequencing (including fragment analysis).

When it comes to using a mouse or rat genome to study human disease, you need to have the best experimental model available to advance your research and propel discovery. That’s where we come in. The Transgenic Core at Children’s Hospital Research Institute, working in partnership with the University of Pennsylvania CRISPR Core Facility, can build complex mouse and rat models, genetically manipulating the mouse and rat genome to meet your specific research needs utilizing cutting-edge and classical genetic engineering approaches.
The Transgenic Core is a service sponsored by the CHOP Research Institution to enable investigators to drive cutting edge basic and bench-to-bedside research. The Mission of the Core is to provide a cost-effective fast method for the generation and preservation of genetically altered mice or rats for the research community. Please visit the Transgenic Core table for more information about the services we offer, we look forward to meeting you.

The Core generates induced pluripotent stem cell (iPSC) lines from somatic cells including peripheral blood mononuclear cells and fibroblasts. The Core has established standard operating procedures for:
1) Pluripotent stem cell growth and maintenance
2) Genome editing technologies including CRISPR-CAS9
3) Differentiation to germ layer and derivative tissues of interest.
The Core provides enrichment training courses for investigators interested in learning how to work with pluripotent stem cells and/or establish the pluripotent stem cell technology in their own labs.

The Human Pluripotent Stem Cell Core, established in 2008 by the Raymond G. Perelman Center for Cellular and Molecular Therapeutics at Children’s Hospital of Philadelphia, serves the research needs of CHOP, the University of Pennsylvania, and outside academic communities in the field of human pluripotent stem cell biology.

The Raymond G. Perelman Center for Cellular and Molecular Therapeutics at The Children's Hospital of Philadelphia has established a state-of-the-art cGMP clinical vector manufacturing suite for both adenoassociated and lentiviral vectors. The facility is under the direction of Han van der Loo, a leading expert in clinical vector production and characterization. Our goal is to help to realize the enormous promise of gene transfer therapy to address unmet medical needs.

The Clinical Vector Core provides manufacturing of clinical and pre-clinical Adeno-Associated Virus (AAV) vectors of serotypes 1, 2, 5, 6, 8, 9, and Lentivirus (LV) vectors. Novel or modified serotypes will require development prior to scale-up. Products for clinical use are manufactured in compliance with Current Good Manufacturing Practices (cGMP) for Phase 1 and 2 clinical trials. To support pre-clinical work, including pharmacology and toxicology studies, we offer products manufactured using a GMP-comparable process. Research-grade products for proof-of- principle and bridging studies are also offered.

The Core Facility uses a patented vector production technology and a highly efficient purification process that uses combined column and gradient centrifugation-based process steps. This system has manufactured clinical-grade AAV vectors that have demonstrated excellent safety in several clinical studies. We are also in the process of implementing GMP Lenti vector production.

Our production efficiency is achieved along with exceptionally high vector product quality. Our final product is highly purified, containing negligible amounts of impurities such as empty capsid. Prior to the final release of the clinical vectors, the vector product is subjected to numerous tests to ensure quality. We also provide federal regulatory documentation and necessary certifications.

Recently, the Clinical Vector Core has also installed Lenti viral vector production capacity. Drawing from both in-house and newly acquired expertise, our Lenti group has quickly implemented an efficient production process that can meet our collaborators' clinical protocol needs.

Our proven track record, consistency, high vector production capacity and world-class expertise have enabled us to achieve national recognition. We served as the designated NHLBI contract laboratory for AAV vector design, cGMP manufacture, and certification from 2007 to 2017, and continue to work with sponsors in government, academia and industry, nationally and internationally.

We are committed to collaborating with investigators to meet their studies’ unique biostatistics and data management needs to ensure that the answers to research questions are supported by valid, statistically sound data and results. Our team of highly motivated and experienced biostatisticians can assist you in the design of experiments, planning of clinical protocols, analysis and interpretation of data, and presentation and dissemination of results. Our data management team members have expertise in designing case report forms, developing databases, creating data management plans, developing metrics to report on study progress, and delivering high quality datasets for analysis.

We also offer free limited consulting for data management and statistical questions.

Our team offers the unique advantage of experience with the submission of a Biologics License Application (BLA). We are available to investigators seeking guidance with clinical trial start-up, oversight, and regulatory submission.

Comparative Medicine Services Core
The Comparative Medicine Services Core provides comprehensive support for nonclinical research programs. Because successful nonclinical development requires thoughtful planning and early strategic alignment, we encourage investigators and sponsors to engage with our team as soon as a drug or device is anticipated to advance toward human clinical trials.
Our Core is staffed by highly trained professionals with the expertise to design, conduct, and oversee a wide range of animal studies. We are committed to the highest standards of animal welfare, scientific rigor, procedural reproducibility, and exceptional customer service. CMSC anticipates developing capacity for GLP-like compliance in the near future.

Comprehensive Support Across the Nonclinical Lifecycle
The Comparative Medicine Services Core offers end-to-end support throughout all phases of your nonclinical study program, including:
• Grant and funding application support
• Budget development and financial planning
• Experimental design and study planning
• Study protocol drafting, implementation, and management
• IACUC protocol guidance and consultation
• Standard Operating Procedure (SOP) development, management, and archiving
• Training delivery and documentation
• Study execution and data generation
• Secure archiving of study materials and data
Areas of Expertise
The Comparative Medicine Services Core specializes in, but is not limited to, the following study types:
• Pharmacokinetic studies
• Biodistribution studies
• Toxicology and reproductive toxicology studies
• Medical device testing
• Surgical model development

The Research Vector Core (RVC) provides premium recombinant adeno-associated viral (AAV) and lentiviral vectors to support basic research and preclinical studies. As part of the Center for Cellular and Molecular Therapeutics at the Children’s Hospital of Philadelphia, the RVC is committed to manufacturing high-quality vectors using optimized, industry-recognized production and purification processes.
With extensive expertise in producing custom vector constructs at multiple scales, the RVC offers state-of-the-art technology, rigorous quality control standards, and expert technical support. Our team partners with investigators to enable efficient, reliable gene transfer and to accelerate translational research and therapeutic development.

The CHOP Engineered Cell Therapy Core (ECTC) provides a resource for researchers with promising proof- of-concept to advance their chimeric antigen receptor (CAR) T or other cell therapy research through all stages of the preclinical process, including design, construction, testing, and validation.

We work with researchers at CHOP, Penn, other academic institutions, and industry to provide a wide variety of laboratory and consultatory services.

Our Core is equipped to support both routine testing and more elaborate collaborative projects. We provide expert guidance in the design, construction, and selection of CARs and other cell therapies against a multitude of targets and diseases. We also offer small-scale lentivirus production and small-scale T cell transduction and expansion for experimental purposes.

Whether your goals are to simply save time on your project or to initiate a collaborative partnership, the ECTC looks forward to advancing your cell therapy research.

The Pathology Core provides histopathology, Immunohistochemistry, tissue microarray, and imaging services to researchers at Children’s Hospital of Philadelphia Research Institute and the surrounding academic community. Our technical and professional staff has extensive experience in all aspects of tissue processing, histological techniques, antibody work-up, and morphologic analysis. In addition, we offer tools to facilitate high throughput analysis of tissue sections and imaging. The Pathology Core is located in the A Level of Colket Translational Research Building (CTRB) Room A410. Our staff is available for consultation, troubleshooting, and assistance in planning and interpreting experiments histopathology and related techniques.

The Flow Cytometry Core Laboratory serves the research community at the Children’s Hospital of Philadelphia and the University of Pennsylvania by providing access to state-of-the-art instrumentation and technical expertise. Located in Suite 1207 of the Abramson Pediatric Research Center, the Core offers a full range of services, including sample preparation, advanced multi-color analysis, and high-speed cell sorting. Our experienced staff delivers personalized training and project-specific consultations to help investigators seamlessly integrate cutting-edge flow cytometry technologies into their research programs.

The Small Molecule and Metabolite Core Laboratory focuses on quantitative bioanalytical assay development, validation and implementation for drugs, metabolites and biomarkers in blood, serum, plasma, urine, ultrafiltrate and microdialysate utilizing mass spectrometry techniques.

As part of the Center for Single Cell Biology, our service core provides convenient access to cutting-edge single-cell, spatial and in situ technologies to CHOP, UPenn and the wider research community. Established in early 2022, we are equipped with state-of-the-art instruments, experienced research assistants and bioinformaticians to offer in-house experimental and computational support to your single-cell research. Our services include:
• 10x Genomics single cell assays
• 10x Genomics Visium CytAssist and Visium HD spatial transcriptomics
• 10x Genomics Xenium in situ spatial transcriptomics
• Vizgen MERSCOPE in situ spatial transcriptomics
• NanoString GeoMx Digital Spatial Profiler RNA and protein assays

We thrive in providing high-quality and cost-effective service work. We are happy to consult with you on how our services can facilitate your researchWe thrive in providing high-quality and cost-effective service work. We are happy to consult with you on how our services can facilitate your research. zhangm5@chop.edu 3501 Civic Center Blvd, CTRB A450D, Philadelphia, PA 19104

Established in 2006, the CAG Genotyping Laboratory is fully equipped with state-of-art liquid handling technology and experienced staff members. The CAG genotyping core offers both standard and custom Illumina array project design. With the capacity to process >2300 samples/week and generate >480 million genotypes per day, the genotyping core fully integrates with our Biorepository and Bioinformatics group, offering the collaborator the opportunity for a seamless experience from DNA extraction to data release.

Established in 2006, the CAG Biorepository is one of the world’s largest and most diverse pediatric biobanks, hosting more than 600,000 biological samples that have been genotyped or sequenced in CAG’s CLIA and CAP-accredited high-throughput centers. This core offers services in DNA and RNA extraction and QC.

Led by experts with more than 10 years of gene therapy clinical trial experience, the CIGT team aims to offer more breakthrough therapies to our patients sooner, by streamlining the startup of complex gene therapy trials and ensuring licensed gene therapies are available in our clinics.

High Throughput Sequencing Core (HTS Core) is a state of the art, full-service facility providing instrumentation, library preparation, and sequencing services to CHOP, UPenn, and external investigators in genomic, epigenomic and transcriptomic studies.

The Small Animal Imaging Facility (SAIF) empowers CHOP researchers with state-of-the-art translational imaging capabilities. Our robust imaging platform integrates multiple modalities—including MRI, PET, CT, Optical, and US—essential for monitoring disease progression and therapeutic response in vivo in small animal models.
The technical director partners with principal investigators to move their science projects forward by:
• Selecting the optimal imaging modality
• Design and optimization of acquisition protocols
• Expert execution of in vivo imaging experiments
• Training for new users on image acquisition
• Advanced data analysis and project management
The SAIF ensures customers with the highest level of technical expertise and translational capability. We offer the tools necessary to bridge preclinical findings to clinical applications.

The LAIF Core facilitates advanced MR image-guided interventional and noninvasive procedures to support research across a broad range of disease areas, including neurodegenerative, cardiothoracic, and reproductive disorders. Our imaging capabilities span structural MRI, diffusion imaging, DCE and ASL perfusion, spectroscopy, angiography, cardiac imaging, tissue elastography, functional imaging, flow quantification, and quantitative T1, T2, and T2* mapping. A major advantage of preclinical MRI is the ability to use imaging methods and pulse sequences that closely parallel those used on clinical scanners, creating a strong platform for seamless translation from bench to bedside.
In collaboration with the Division of Veterinary Resources (DVR), we encourage investigators to consult with our teams on all scientific, medical, technical, and compliance aspects of studies involving large animal models. Investigators are expected to obtain Institutional Animal Care and Use Committee (IACUC) approval before initiating study activities.
Beyond image acquisition, the LAIF Core provides comprehensive data processing, post-processing, and quantitative image analysis support to help investigators extract meaningful outcomes from complex imaging datasets. These services include image reconstruction workflows, multimodal image registration, segmentation, volumetric and regional quantification, diffusion and tract-based analysis, spectroscopy processing, and development of customized pipelines tailored to specific study needs. We also support investigators in generating high-quality preliminary data for grant applications, instrument proposals, and translational research initiatives by helping design imaging strategies, optimize acquisition protocols, and deliver rigorous quantitative analyses that strengthen scientific aims.
For larger research programs, the LAIF Core can assist with processing and managing large-scale imaging datasets to support longitudinal studies, multisubject analyses, and publication-ready results. Our goal is to provide investigators with robust imaging, analytical, and consultative support that advances discovery, strengthens competitiveness for external funding, and accelerates dissemination of impactful research findings.

The Zebrafish Core offers all resources for zebrafish research and provides fish husbandry. We design and perform experiments, teach zebrafish techniques and advice and support researchers. Our special expertise disease modeling by creation of mutant and transgenic lines, analysis of disease phenotypes, and drug testing.

The Gastrointestinal Epithelium Modeling (GEM) Core is a component of the GEM Program - a collaborative research effort focused on accelerating discovery and innovation using patient tissue-derived organoids. GEM Core staff generate and maintain a living biobank of tissue-derived organoids with matched original tissue and blood specimens and provide access to specialized training, protocols, and reagents.

The CHOP Biorepository Resource Center (BioRC) serves to accession, process, store, and manage distribution of research biospecimens for biobanking efforts. We offer specimen processing, and RNA and DNA extraction services.

The Proteomics Core facility specializes in bottom-up, mass spectrometry-based proteomics with a commitment to quality, rigor, problem-solving, and innovation. Our goal is to provide expert guidance to the scientific community on optimizing the use of this technique for answering biological questions and to generate top-tier mass spectrometry-based proteomics datasets.