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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

Software R/Shiny application for interactive creation of Circos plot. Used for creation of Circos plot interactively.

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• RRID
• 4 years ago - by Anonymous

Shared Resource that offers bioinformatics and informatics services for basic research and clinical projects.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Closed loop automated reaching apparatus for interrogating complex motor behaviors.Mechanical components include behavior box, series of cameras, and food pellet dispenser. Single workstation computer manages cameras, communicates with microcontroller, and analyzes mouse behavior in real time using modules extracted from DeepLabCut. Integrates fully automated, markerless kinematic tracking of multiple features to classify animal behavior and delivers neural stimulation based on behavioral outcomes. CLARA is compatible with advanced neurophysiological tools, enabling testing of neurostimulation devices and identification of novel neurological biomarkers.System fully automates trial initiation and pellet delivery and is capable of accurately delivering stimulation in response to trial outcome with short latency.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Software pipeline for video analysis. Deep learning Swiss knife for behavioral data analysis.Performs segmentation, identification, pose-estimation and classification of complex behaviour. Used for analysis of behavior of multiple animals in complex environments.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

System uses Arduino microcontroller to control relay module that operates solenoid valve which all sit in 3D printed housing. Solenoid works in conjunction with flowmeter regulator to allow for controlled flow of pressurized air into target. Timing of distensions is controlled via either custom Python based UI, or by triggered TTL pulse.Timed pressure control hardware and software used for delivery of air mediated distensions in animal models.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Software tool as multi subject keypoint detection library for real time pose estimation.Used to track behavior of monkeys in natural environments, without disrupting their typical pattern of behavior. Deep learning software system for body, face, hands, and foot estimation in monkeys.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Open source animal tracking software tool. Used to visually track movement of multiple animals at once.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth