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http://harvard.eagle-i.net/i/0000012d-56f2-62b7-2162-17a280000000

Core facility that provides the following services: Ultrasound/sonography access service. Ultrasound, which is also known as sonography, is a painless, non-invasive imaging technique that lets us look inside your child''s body without the use of radiation. It uses high-frequency sound waves to create pictures of organs, bones, tissues and blood vessels.

Proper citation: CHB Ultrasound (RRID:SCR_009608) Copy   

•   Source: SciCrunch Registry
  

http://eagle-i.itmat.upenn.edu/i/0000013b-9b4b-434b-83a0-df0880000000

Core facility that provides the following services: Tissue microarray construction service, Unstained slides preparation service, H&E staining (on unstained slide) service, Special stain (from slide) service, TUNEL labeling service, IHC stain from slide service, In situ hybridization RNAscope service, New antibody workup service, Decalcification service, Laser capture service, Histopathology-related techniques training, Histopathology technical consultation service, Basic imaging workstation access, Laser capture microdissection microscope access. The Pathology Core Laboratory at the Children''s Hospital of Philadelphia Research Institute provides basic histopathology, research immunohistochemistry, tissue microarray, and laser capture microdissection services to researchers at Children''s Hospital and within the surrounding academic community. We are located on the 7th Floor of the Leonard and Madlyn Abramson Pediatric Research Center in room 706. The Pathology Core Laboratory unites three core components in a single core facility: histopathology, tissue microarray and laser capture microdissection. The core offers a full range of histopathology services including tissue processing, embedding, and cutting, for both paraffin and frozen tissue. We also perform most standard stains as well as immunohistochemistry, antibody workup, fluorescence, in situ hybridization and TUNEL. Tissue microarrays can be constructed using a Beacher Arrayer. Sophisticated imaging instrumentation is available for virtual microscopy (ScanScope from Aperio) and image analysis (Image ProPlus, Volocity). Specialized software is available to image and analyze tissue microarrays, and to manage and store array data.

Proper citation: CHOP Pathology Core Laboratories (RRID:SCR_009729) Copy   

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https://www.research.chop.edu/flow-cytometry

Core provides access to instrumentation and technical expertise. Offers services, including sample preparation, advanced multi-color analysis, and high-speed cell sorting. Our experienced staff delivers personalized training and project-specific consultations.

Proper citation: Children's Hospital of Philadelphia Flow Cytometry Core Facility (RRID:SCR_009726) Copy   

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http://nac.spl.harvard.edu/

Biomedical Technology Resource Center that develops image processing and analysis techniques for basic and clinical neurosciences. The NAC research approach emphasizes both specific core technologies and collaborative application projects. The core activity of the center is the development of algorithms and techniques for postprocessing of imaging data. New segmentation techniques aid identification of brain structures and disease. Registration methods are used for relating image data to specific patient anatomy or one set of images to another. Visualization tools allow the display of complex anatomical and quantitative information. High-performance computing hardware and associated software techniques further accelerate algorithms and methods. Digital anatomy atlases are developed for the support of both interactive and algorithmic computational tools. Although the emphasis of the NAC is on the dissemination of concepts and techniques, specific elements of the core software technologies have been made available to outside researchers or the community at large. The NAC's core technologies serve the following major collaborative projects: Alzheimer's disease and the aging brain, morphometric measures in schizophrenia and schizotypal disorder, quantitative analysis of multiple sclerosis, and interactive image-based planning and guidance in neurosurgery. One or more NAC researchers have been designated as responsible for each of the core technologies and the collaborative projects.

Proper citation: Neuroimage Analysis Center (RRID:SCR_008998) Copy   

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https://scicrunch.org/Kravitz

The data sets included in this resource are published in Kravitz et al, 2012 Distinct roles for direct and indirect pathway striatal neurons in reinforcement (Nat. Neurosci). The data shows: optogenetic activation of dopamine D1 or D2 receptor-expressing striatal projection neurons influenced reinforcement learning in mice. Stimulating D1 receptor-expressing neurons induced persistent reinforcement, whereas stimulating D2 receptor-expressing neurons induced transient punishment. These 3 recording files contain data collected in 2010 and 2011 by Lex Kravitz in Anatol Kreitzer''s lab at the Gladstone Institutes. Each file contains ~ 1 hour of awake in vivo recording data, containing the spike times for ~30 minutes of spontaneous activity, preceeded or followed by 400 laser pulses (473nm laser light, 1 sec pulses, 3 seconds inter-pulse-interval). The laser pulses were presented at 4 intensities: 0.1mW, 0.3mW, 1.0mW, and 3.0mW, and pulse times at each intensity are given in separate columns in each data file. Finally, each data file contains the identification of ''light-modulated units'' as we identified them (see methods below). Methods: Viral expression of DIO-ChR2-YFP and DIO-YFP We used double-floxed inverted (DIO) constructs to express ChR2-YFP fusions and YFP alone in Cre-expressing neurons, which virtually eliminates recombination in cells that do not express Cre-recombinase (Sohal et al, Nature, 2009). The double-floxed reverse ChR2-YFP or YFP cassette was cloned into a modified version of the pAAV2-MCS vector (Stratagene, La Jolla, CA) carrying the EF-1a promoter and the Woodchuck hepatitis virus posttranscriptional regulatory element (WPRE) to enhance expression. The recombinant AAV vectors were serotyped with AAV1 coat proteins and packaged by the viral vector core at the University of North Carolina. The final viral concentration was 4 x 10^12 virus molecules/mL (by Dot Blot, UNC vector core). This viral construct can now be ordered in single aliquots directly from UNC Vector core as product AAV-EF1a-DIO-hChR2(H134R)-EYFP, at http://genetherapy.unc.edu/services.htm) Implantation of electrode arrays for awake recordings Anaesthesia was induced with a mixture of ketamine and xylazine (100mg ketamine plus 5mg xylazine per kilogram of body weight i.p.) and maintained with isoflurane through a nose cone mounted on a stereotaxic apparatus (Kopf Instruments). The scalp was opened and a hole was drilled in the skull (0.0 to +1.0mm AP, -1.0 to -2.0mm ML from bregma). Two skull screws were implanted in the opposing hemisphere. Dental adhesive (C&B Metabond, Parkell) was used to fix the skull screws in place and coat the surface of the skull. An array of 16 or 32 microwires (35-��m tungsten wires, 100-��m spacing between wires, 200-��m spacing between rows; Innovative Physiology) and one optical fiber in a ferrule was lowered into the striatum (3.0mm below the surface of the brain) and cemented in place with dental acrylic (Ortho-Jet, Lang Dental). After the cement dried, the scalp was sutured shut. Animals were allowed to recover for at least seven days before striatal recordings were made. In vivo electrophysiology Voltage signals from each recording site on the microwire array were band-pass-filtered, such that activity between 150 and 8,000Hz was analysed as spiking activity. This data was amplified, processed and digitally captured using commercial hardware and software (Plexon). Single units were discriminated with principal component analysis (OFFLINE SORTER, Plexon). Two criteria were used to ensure quality of recorded units: (1) recorded units smaller than 100��V (~3 times the noise band) were excluded from further analysis and (2) recorded units in which more than 1% of interspike intervals were shorter than 2ms were excluded from further analysis. Average waveforms were exported with OFFLINE SORTER. During the recording we coupled the array to a laser and pulsed the laser at four intensities (0.1mW, 0.3mW, 1mW, and 3mW). Laser stimulation was run in a cyclical fashion, on for 1 second, and off for 3 seconds. Each neuron received 100 pulses at each laser intensity. Identification of ChR2 expressing units in in vivo recordings For all neurons, peri-event histograms were generated for each laser intensity independently. Neurons were classified as ChR2-expressing if they exhibited a firing rate greater than 3x above the standard deviation of the 1-second preceding the laser pulse within 10msec of the laser onset. Each neuron was tested independently at each laser power, and neurons that satisfied this criteria at any one power were defined as ChR2-expression.

Proper citation: Kravitz Dataset1 (RRID:SCR_008759) Copy   

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http://eagle-i.itmat.upenn.edu/i/00000142-47d2-2012-91c7-0c6080000000

The Clinical and Translational Research Center (CTRC) offers ophthalmological testing services for children. The Ophthalmology Core at CHOP?s CTRC was established t**provide clinical and translational research services in ophthalmology for the assessment of visual function and structure. Services provided include: * Eye exams (includes visual, recognition and grating acuity; anterior segment, fundus exam, refraction) **Contrast sensitivity **Color vision testing * Optical coherence tomography (OCT) tests of the: **Anterior segment **Posterior segment ? optic nerve **Posterior segment ? retin A* Visual field measures: **Using Humphrey **Using Goldman * Full field sensitivity testing * Electroretinography * Visual evoked potential * Fundus photography * Ocular ultrasound * Professional interpretation of all tests is als**available

Proper citation: CHOP CTRC Ophthalmology Core (RRID:SCR_009724) Copy   

•   Source: SciCrunch Registry
  

http://eagle-i.itmat.upenn.edu/i/0000013a-bc4e-ecdd-d69a-d90d80000000

Core facility that provides the following services: Clinical trials consultation service, Document storage service, Investigational new drug or investigational device exemption application support service, Institutional Review Board submission service, Additional regulatory submissions support service, Protocol development service, Human subject recruitment support service, Study feasibility service, Study placement service. The Clinical Trials Office (CTO) at The Children''s Hospital of Philadelphia is a centralized office that provides resources and assistance to clinical research investigators, enabling them to carry out clinical research in a manner consistent with the Hospital''s goals ? excellent patient care, top-quality education, and innovative research. The CTO has expertise in implementing, conducting, and monitoring clinical trials and provides a variety of services that benefit both novice and experienced clinical researchers. The CTO is designed to ensure the excellence and compliance of an investigator''s clinical research trial. The Children''s Hospital of Philadelphia established the CTO in 1999 as part of the institution''s emphasis on clinical research. Since then, the CTO has experienced rapid growth. The CTO advances the quality and quantity of clinical research at Children''s Hospital and its associated network. Specifically, the CTO supports research at the Hospital by developing and completing submissions to the Hospital''s Institutional Review Board; assisting in the preparation of Investigational New Drug and Investigational Device exemption application submissions to the Federal Drug Administration; conducting clinical research studies under the guidance of principal investigators; and developing budgets and providing research training for investigators, study coordinators, and administrative staff. The CTO staff works in partnership with investigators to ensure the protection of human subjects in accordance with Good Clinical Practice, federal, state and/or local regulations and the requirements of the study sponsor.

Proper citation: CHOP Clinical Trials Office (RRID:SCR_009725) Copy   

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http://neurogeometry.net/

Data set of connection probabilities and PSP amplitudes from Chapeton, J., Fares, T., LaSota, D., and Stepanyants, A., Efficient associative memory storage in cortical circuits of inhibitory and excitatory neurons, PNAS, 109(51): E3614E3622 (2012). Available as a PDF under Resources tab.

Proper citation: experimental studies reporting connection probabilities and/or unitary PSP amplitudes (RRID:SCR_008995) Copy   

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http://www.sr-research.com

THIS RESOURCE IS NO LONGER AVAILABLE,documented on February 1st, 2022. Instrument supplier providing eye tracking capabilities for behavioral labs as well as for MRI, MEG, and EEG research environments.

Proper citation: SR Research EyeLink Eye Trackers (RRID:SCR_009602) Copy   

•   Source: SciCrunch Registry
  

http://eagle-i.itmat.upenn.edu/i/00000142-3843-baeb-91c7-0c6080000000

The Nutrition Assessment Unit of the Nutrition Core is a state-of-the-art facility for the assessment of growth and body dimensions, body composition (the amount of muscle, fat and bone in the body), energy expenditure, bone density, and muscle strength. The Unit has two locations and four experienced technicians for performing research assessments.

Proper citation: CHOP CTRC Nutrition Core Nutrition Assessment (RRID:SCR_009723) Copy   

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http://eagle-i.itmat.upenn.edu/i/00000138-7cdd-51df-fbab-3b8480000000

Core facility that provides the following services: Data management/information technology subcore services, Statistical analysis and database consulting service, Limited statistical analysis service. The Biostatistics and Data Management Core (BDMC) at The Children''s Hospital of Philadelphia (CHOP) supports investigators from virtually all subspecialties of pediatric medicine and supports studies ranging from small, narrowly defined basic science projects to large, multi-site clinical trials. The Biostatistics and Data Management Core currently supports more than 50 funded studies and collaborates with investigators on numerous grant applications each year. The BDMC is staffed by a Scientific Director, Deputy Director, and data management/information technology managers, as well as approximately 20 additional staff members representing the disciplines of biostatistics, data management, information technology and administration. The BDMC is located on the CHOP campus (3535 Market Street), and is operated and supported by Westat, a large health research organization with extensive biostatistics, data management and information technology capabilities.

Proper citation: CHOP Biostatistics and Data Management Core (RRID:SCR_009720) Copy   

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http://snyderome.stanford.edu/

Data set generated by personal omics profiling of Dr. Michael Snyder at Stanford University. It combines genomic, transcriptomic, proteomic, metabolomic, and autoantibody profiles from a single individual over a 14 month period. The analysis revealed various medical risks, including type II diabetes. It also uncovered extensive, dynamic changes in diverse molecular components and biological pathways across healthy and diseased conditions.

Proper citation: iPOP (RRID:SCR_008991) Copy   

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http://gemstone.mozdev.org

Integrated framework for accessing grid resources that supports scientific exploration, workflow capture and replay, and a dynamic services oriented architecture. This framework provides researchers in the molecular sciences with a tool to discover remote grid application services and compose them as appropriate to the chemical and physical nature of the problem at hand. The initial set of application services include molecular quantum and classical chemistries (GAMESS, APBS, Polyrate), along with supporting services for visualization (QMView), databases, auxillary chemistry services, and documentation and education materials. * Rich-client Desktop Interface - Gemstone is a Firefox extension that provides a dynamic user interface to backend computational, data and visualization services. * Workflow Integration - Gemstone supports a workflow component based on Informnet (see http://grid-devel.sdsc.edu/informnet). They are adapting the Informnet workflow engine to support workflow publication and discovery, brokering, and fault tolerance. They are also adding support for automatic generation of workflows based on user interaction. * Strongy Typed Data Schemas - They are working extensively with CML, integrating their data schemas into workflow systems and providing bridges to the GamesXML that they defined.

Proper citation: Grid Enabled Molecular Science Through Online Networked Environments (RRID:SCR_008629) Copy   

•   Source: SciCrunch Registry
  

http://harvard.eagle-i.net/i/0000012d-b8f4-ce9f-4882-b08d80000000

Nuclear Medicine and Molecular Imaging performs non-invasive, painless imaging tests that can reveal important information about your child''s health. Nuclear medicine uses short-lived radiopharmaceuticals and specialized cameras to create images of the human body. The images show blood flow and functional and metabolic activity within organs and lesions. This technology allows early diagnosis and monitoring of disease and can often make invasive procedures unnecessary. It also complements information obtained from X-rays, computed tomography (CT), ultrasound, and magnetic resonance imaging (MRI). Some applications of nuclear medicine are used for treatment of certain specific diseases.

Proper citation: CHB Nuclear Medicine and Molecular Imaging (RRID:SCR_009717) Copy   

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https://github.com/BRAINSia/BRAINSTools/tree/master/TestData

About 1.2GB of anonymized imaging data of many different file formats used by the BRAINS suite of tools (BRAINSFit, GTRACT, BRAINS, BRAINSTracer... and others) as a common set of anonymized data for nightly regression testing.

Proper citation: BRAINSTestData (RRID:SCR_009517) Copy   

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http://www.dartmouse.org

Core facility that provides the following services: Medium-density speed congenic backcross service, Medium-density genetic background check service, DNA extraction. DartMouse is a not-for-profit core facility funded by the National Institutes of Health''s National Center for Research Resources. The mission of DartMouse is to facilitate the development of congenic mice in support of pre-clinical projects across the United States. Use of DartMouse allows the generation of congenic mice in 5 generations (~1.5 years), versus the 10 generations (~3 years) required by conventional back-crossing. Facility staff provides expert advice on mouse speed congenic development, mouse genetic background analysis, and mouse genetic mapping. Investigators provide us with mouse tail clippings. From these, DartMouse isolates genomic DNA and performs and analyzes complete genome-wide scans. We return data in graphical and spreadsheet formats, and make specific recommendations on breeder selection. We operate an Illumina BeadStation 500. Chips use a 1449 SNP array covering the mouse genome with an average density of <5 cM.

Proper citation: DartMouse - Speed Congenics (RRID:SCR_009757) Copy   

•   Source: SciCrunch Registry
  

http://harvard.eagle-i.net/i/0000012e-a5a7-396c-55da-381e80000000

Core facility that provides the following services: Genome-scale screening of lentiviral human and mouse shRNA libraries.

The RNAi Screening Facility provides investigators with access to RNAi reagents and high-throughput screening technology. Lentiviral-based RNAi constructs against the human and mouse genomes are provided by the RNAi Consortium of the Broad Institute, and can be used to transduce a wide range of target cells, including primary and non-dividing cells. The Facility provides reagents, equipment, and technical expertise to design, optimize, and perform cell-based, arrayed lentiviral RNAi screens. Additionally, lentiviral RNAi constructs against individual genes can be requested.

Proper citation: DFCI RNA Interference Screening Facility (RRID:SCR_009755) Copy   

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http://harvard.eagle-i.net/i/0000012c-cca8-e37a-a061-4a6580000000

The Molecular Diagnostics Laboratory provides such research services as microRNA expression profiling, human cell line identity verification, mutation detection for clinical research studies, and specimen processing for clinical research studies to investigators at the Dana Farber Cancer Institute, as well as to investigators at other institutions. Consultation on experimental design and assistance with data analysis are also available.

Proper citation: DFCI Shannon McCormack Advanced Molecular Diagnostics Laboratory (RRID:SCR_009756) Copy   

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http://mbcf.dfci.harvard.edu

Core offers services for genomic next-generation sequencing library preparation, sequencing and analysis applications including RNAseq, ChIPseq, ATACseq, CRISPR screening, whole genome methylation profiling, targeted resequencing, single-cell RNAseq, exome sequencing, and more. Performs bioinformatics analysis such as integration of multi-omics datasets or specialized analyses. Genomics core technology platforms include Illumina NovaSeq6000, NextSeq500s, MiSeqs, MiniSeq. High throughput sample preparation is performed on Beckman Coulter Biomek FX and i7 systems. Low throughput samples are prepared by technical staff.

Proper citation: Dana-Farber Cancer Institute Molecular Biology Core Facility (RRID:SCR_009754) Copy   

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http://harvard.eagle-i.net/i/0000012f-bbba-4d59-de5a-673e80000000

Core facility that provides the following services: Cell Sorting.

The Flow Cytometry Core Facility provides sterile sorting and analysis of samples in support of research at DFCI. The core has 2 high-speed cell sorters, the BD FACSAria II SORP and BD FACSAria IIu with up to 12-color simultaneous detection utilizing multi-laser platforms. Sample populations can be sterile sorted into a variety of tubes or plates. The BD FACSAria II SORP and BD FACSAria IIu are both equipped with the Automated Cell Deposition Unit (ACDU) for sterile sinlge cell sorting into 96, 384 micro titer plates. The core presently has 2 analyzers, the BD LSRFortessa SORP and BD LSRII with up to 12-color simultaneous detection utilizing multi-laser platforms. The BD LSR II is also equipped with an HTS(high throughput sampler) for analyzing samples directly from 96 well micro titer plates as well as being able to run 5ml tubes. The Facility staff is available to assist researchers with their sorting and analysis needs. Researchers who would like to utilize the analyzers are trained so that they can analyze their experiments independently. The staff will assist with data acquisition and analysis as well as interpretation. They will also assist in experiment design and implementation as well as troubleshooting. Training sessions are available for researchers who would like to run their sorting experiments independently.

Proper citation: DFCI Flow Cytometry Core Facility (RRID:SCR_009751) Copy   

•   Source: SciCrunch Registry