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Provides specimens including gynecologic cancer specimens such as fresh and frozen tissues, plasma, serum, peripheral blood mononuclear cells, blood, formalin fixed paraffin embedded (FFPE) samples, and Tissue Microarrays (TMAs). All samples collected have clinical annotation including demographic patient profiles, pathological and clinical notations, treatment history, and detail disease information, etc. We are building and maintaining centralized research database according to HIPPA specifications and Penn IRB standards.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Core provides equipment and services to investigate behavior phenotypes of models related to neurological and other disorders. Core is utilized by scientists across disciplines that are interested in behavioral consequences of unique physiological disruptions (e.g., metabolic, drugs etc.). Provides assessment of many domains of behavior including sensory, motor, social, communication, affect related behaviors and learning and memory. NTC was established in 2012 through generous startup funds from the Penn School of Medicine, the Institute for Translational Medicine and Therapeutics (ITMAT), Center for Sleep and Circadian Neurobiology (CSCN) and Penn Medicine Neuroscience Center (PMNC).

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Core provides comprehensive suite of imaging modalities including magnetic resonance imaging (MRI), spectroscopy (MRS), optical imaging (including bioluminescence, fluorescence, and near-infrared imaging), computed tomography (CT), positron emission tomography (PET), single photon emission computed tomography (SPECT), and ultrasound (US). In addition, dedicated housing is available for mice and rats undergoing longitudinal imaging studies. Ancillary facilities and resources of SAIF are devoted to radiochemistry and image analysis.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Our core, which is part of the PennCHOP Microbiome Program, provides access for researchers to small experimental isolators for variety of in vivo studies using germ free mice. Core personnel provide technical support for germ-free experiments. New addition to core is state-of-the-art Isocage system.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 8th,2024. Facility offers sequencing services on three platforms, gold standard Sanger sequencing on ABI capillary sequencers, next generation sequencing (NGS) on Ion Torrent PGM and S5 and, Illumina MiSeq along with experimental design and data analysis.NGS service includes library preparation for multiple applications including targeted sequencing, RNA-Seq and Exome-Seq. Capillary sequencers also enable microsatellite genotyping and fragment analysis for VNTR, SNaPshot and Human Cell Line Authentication. Molecular biological services include PCR, cloning, subcloning, mutagenesis, construct preparation and, plasmid DNA preps at different scales.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 10,2025. Core provides services related to single cell and bulk whole genome, RNA-Seq, ATAC-Seq, BIS-Seq, Exome-Seq, ChIP-Seq, CLIP-Seq, etc.Provides Illumina NovaSeq 6000 in addition to NextSeq and MiSeq sequencers - which all feature self-service as well as full-service operation. Offers experience with difficult, low input samples as well as sequencing and analyzing novel library types. Small Oxford Nanopore sequencer allows for full-length RNA or cDNA sequencing as well as very long read (100KB) sequencing from genomes. Offers experimental design services prior to starting your experiment.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Core is overseen by Cardiovascular Institute and is partnership with the Abramson Cancer Center and the Institute for Diabetes, Obesity and Metabolism at Penn. Provides expertise in targeted and untargeted metabolomics of biological samples using liquid chromatography/mass spectrometry. Performs assays and assists in interpretation of results.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Core provides wet bench expertise and infrastructure support for early phase�clinical trials and other investigations. Offers purified cell subsets from healthy human apheresis donors. �HIC staff are qualified to�perform blood (PBMC)�and tissue processing for viable cryopreservation following validated�standard operating procedures. Offers�range of immunological assays including digital ELISA, ELISA, ELISPOT, Luminex, flow cytometry and immune repertoire profiling (NGS of BCR and TCR rearrangements in bulk and single cell formats).Offers investigators expertise and guidance in clinical trial sample processing, regulatory compliance, immunology assay design and validation, data analysis and grant writing support.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Core provides distribution of lentivirus based shRNA and cDNA plasmid DNA clones; technical expertise in developing biological assays (i.e. biochemical-, cell-, and high-content) in miniaturized, multiwell microtiter plates that are laboratory automation compatible; high-throughput chemical and functional genomic screening, including data analysis and interpretation. Our goal is to use cutting biological models to discover genes and small molecules that enable scientists to further study functions of poorly understood proteins, signaling pathways, and cells in complex biological process relevant to human physiology and disease.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Core facilitates use of CRISPR/Cas9 genome editing technology to generate novel mouse genetic tools.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Core provides services to users for performing precision, image guided radiotherapy with both Photons and Protons (including FLASH proton radiotherapy) on cells, rodents and larger animals. Physicists will provide expert dosimetry and treatment planning capabilities. Instrumentation consists of two image guided SARRP 200 Small Animal Radiation Research Platforms (Xstrahl) capable of irradiating rodent tissues from 1 mm-20 mm in diameter; research proton beamline (IBA, Roberts Proton Center); one X-RAD 320ix cabinet x-ray irradiator (Precision X-Ray); and two Cs gamma-ray irradiators (Shepherd Mark I), suitable for whole body radiation of rodents.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Flow cytometry shared resource laboratory at the University of Pennsylvania. Facility has instruments, which include analyzers, cell sorters, small particle detectors, dual fluorescence cell counter/viability instrument, tissue dissociator for cell preparation. Provides on-site and off-site support to instrument users, including analyzer and cell sorter training. Core's Research and Development team collaborates/consults with principal investigators in developing high-dimensional panels, as well as staining, acquisition, and analysis.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Training and service facility dedicated to providing both conventional transmission electron microscopy of cells and tissues and state of the art cryo-electron microscopy and cryo-electron tomography for structural investigation of macromolecules and cells.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Core provides bioinformatics services that include data analysis and consultation and building of efficient pipelines that handle various biomedical data including Next-Generation Sequencing (NGS) data.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Core provides personalized assistance on all aspects of imaging, from tips on sample preparation to training on one of our microscopes to assistance with image data analysis. Facility houses confocal microscopes, Bruker Vutara 352 super resolution system, Zeiss Z.1 Lightsheet system, three widefield light microscopes, and several computers dedicated to image processing and analysis. Offers scanning electron microscope sample preparation and imaging.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Facility offers procedural and animal housing to perform in vivo research with biosafety level 3 pathogens, such as SARS-CoV-2. Services include consultation, specialized training, and basic/advanced technical services. Provides equipment to longitudinally monitor mice over course of infection. Animal housing space includes three ABSL-3 separate housing cubicles with Allentown BCU-2 animal cages. Animals will be housed under pathogen free conditions at AAALAC accredited University Laboratory Animal Resources facilities within Vernon and Shirley Hill Pavilion using animal protocols approved by Institutional Animal Care and Use Committee.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Software tool for imputing missing values restoring structure of large biological datasets.Method that shares information across similar cells, via data diffusion, to denoise cell count matrix and fill in missing transcripts.

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• RRID
• 4 years ago - by Anonymous

Software tool as automatic approach for identification of players in biosynthesis pathway. Used for automatic annotation of flavonoid biosynthesis steps in new transcriptome of genome sequence assembly. Various enzymes of entire metabolic networks can be identified if sufficient knowledge about functionally relevant amino acids is available.Combines comprehensive sequence similarity analyses with inspection of functionally relevant amino acid residues and domains in subjected peptide sequences.

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• RRID
• 4 years ago - by Anonymous

PCDC brings together clinical, genomic, and imaging data from institutions around the world to transform pediatric cancer research and outcomes. Headquartered at University of Chicago, PCDC works with international leaders in pediatric cancers and National Cancer Institute to develop and apply uniform data standards that facilitate collection, combination, and analysis of data from many different sources. PCDC Consortium developes common core data dictionary and common governance structure spanning pediatric cancers neuroblastoma, soft tissue sarcoma, acute myeloid leukemia, acute lymphoblastic leukemia, germ cell tumors, bone tumors, and Hodgkin lymphoma to enable innovative cross disease research as well as set standard for future cancer data commons endeavors.

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• dkNET
• 4 years ago - submitted by Maryann Martone

Software package for removing biases across multiple Hi-C datasets. Properly handles Hi-C-specific decay of chromatin interaction frequencies with increasing distance between interacting regions.

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• RRID
• 4 years ago - by Anonymous