Curator Dashboard

Open access database for all cognitive data collected from touchscreen related tasks. Performs data comparison and interactive data visualization for any data uploaded onto the site. There are also guidelines and video tutorials available.

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• NIF
• 7 years ago - submitted by Maryann Martone

Flow cytometry facility offering training and services including:Access to two, 17-color BD LSR II analytical instruments with High Throughput Sampler (HTS) module,Configurations:LSRII 1,LSRII 2;Help with Flow Cytometry Panel Design;Fluorofinder (access our cytometers under CFAR Immunology Core);BD Panel designer;SFGH LSRII Flow Core Protocols;LSRII Startup and Shutdown;How to run the CST calibration assay;Access to a 17-color BD FACSAria II for fluorescence-activated cell sorting (FACS);4-way tube sorting;96 well plate sorting;Index sorting;SFGH ARIA Flow Core Protocols and configuration;ARIA Startup;Determining Drop Delay;Side Stream Set Up;Clog Procedure;ARIA Shutdown Protocol;ARIA Configuration;DNA analysis with standard dyes;Analysis of CFP, GFP, YFP, mRFP, mTomato, and mCherry gene expression proteins;Calcium flux measurements using Indo-1;Training of users on the operation of instruments and experimental design through the CIL Flow Cytometry Course;Maintaining and Upgrading Instruments;Research Support Services (study design, assay selection, grant and paper writing support).

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Core provides ES cell services with high probability of germline transmission. Offers ES cell targeting, genomic DNA extraction from 96-well plates, expansion of targeted ES cells, chromosome counts, and preparation of ES cells for microinjection.Prior to initiation of project, consultation is available on entire procedures of generating knockout mice. Core works with Gladstone Transgenic Gene Targeting Core for your microinjections to deliver full-range gene targeting service;CRISPR gRNA cloning,Cell-based functional test to identify best-performing TALENs or sgRNAs for your gene-editing experiment via mismatch-based assays such as Surveyor or T7E1;In vitro RNA synthesis - can help to make RNAs for your zygote injection or RNA transfection. We have TALEN and Cas9 plasmids with either T7 or T3 promoter subcloned in for efficient in vitro synthesis.sgRNAs for CRISPR can be synthesized off T7-sgRNA PCR product. Quality of synthesized RNAs will be checked via bioanalyzer;Custom TALEN to make double-strand breaks in genome;ES cell targeting (feeder-independent).Investigators targeting construct will be electroporated by core personnel. We have two feeder-independent ES cell lines, E14 (129-derived) and JM8A3.N1 (C57BL/6-derived) you can choose from. After drug selection for about one week, up to 300 colonies will be picked. When they are about to be confluent, we will split them as duplicate, one master plate to freeze for future expansion of positive clones and one plate for genotyping to identify targeted ES cell clones. Your plates for genotyping will be ready for pick-up 2-3 weeks after electroporation date.Genomic DNA extraction from ES cells on 96-well plate;Expansion of targeted clones from core targeting (up to 5 clones),A maximum of 5 positive clones will be thawed from 96-well plates and expanded to 6-wells. We will freeze 5 vials (each about 1 million)/clone for future use and give you 1 vial-equivalent cells to validate your genotyping before injection. It takes about 10 days to expand and freeze down cells;Expansion of ES cells from outside resources (per clone) Investigators provide one vial of frozen ES cells with information about culture condition from original resource. We will revive, nurture, and refreeze ES cells (5 vials) when they are ready. In addition, we will give you 1~2 million cells for your genotyping verification;Preparation for microinjection;Chromosome counting;Custom services.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Core is equipped with two benchtop analyzers from BD Immunocytometry Systems (3 laser/8 color BD Canto II and 4 laser/17 color BD LSR II). These instruments support large variety of applications, including multicolor cell phenotyping, apoptosis, cell cycle and bead arrays. After orientation and training, equipment is available for use directly by investigators. Alternatively experiments can be run and analyzed by Core Facility staff.For sorting purposes facility is equipped with high speed BD FacsAria IIu sorter (4 laser/11 colors), as well as magnetic sorter (AutoMacs Pro) from Miltenyi Biotech. FacsAria IIu is enclosed in Baker Bioprotect III to support sort of biohazardous agents level 1 and 2.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Core provides equipment used for structural modeling in crystals and in solution, using X-ray diffraction and scattering, as well as magnetic resonance.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Core provides service support to all MIT investigators who utilize specialized in vitro cells such as stem cells, organoids, or primary cell lines and/or novel mouse models to study human diseases such as cancer. Projects involve generation of new model system, such as CRISPR-mediated gene editing in mouse to introduce mutation that mimics one found in patients. Helps with projects required optimization of finicky cell cultures and other challenges.Provides customizable set of service options to match specific needs of each project, including consultative advice and troubleshooting, complete tissue culture and microinjection services within our facilities or hands-on training to enable investigators to perfom these experiments either at their own laboratory or within our facilities.Services Include:Gene Targeting genomic modification through traditional or CRISPR/Cas9 locus targeting, assistance with targeting strategies and vector designs;Embryonic Stem Cells generation of new ES lines from mouse strains, importation and testing of lines from outside sources, differentiation of ES lines into specific cell lineages or cell types and more;Microinjection injection of mouse ES cells into blastocysts to generate chimeras and injection of DNA, RNA or CRISPR RNPs into the pronucleus of fertilized mouse eggs to generate transgenic and edited mice;Specialized Tissue Culture establishemnt of new primary cell cultures from a tumor, tissue or organ; Isolation of fibroblasts (MEFs) from mice for culture and analysis;Tissue Culture for Xenograft and Syngenic Modeling optimization, validation and testing of cell lines for orthotopic placement into mice, coordinated with Preclinical Testing Facility;Repository of Reagent Mice Commonly used wild type mice such as C57BL/6j as well as KrasG12D-based models of cancers are maintained on campus for efficient distrubution;Training and Troubleshooting for all aspects of embryonic stem cells, primary cultures, animal breeding etc.;Serum, DMEM, LIF and other media components that have been tested and verified for use with ES cells.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Core provides equipment and technical expertise for evaluation of molecular and morphological changes in cells, tissues, and organs following exposure to complex environmental contaminants. Provides equipment, including automated tissue processor, paraffin embedding center, two automated microtomes, cryostat, vibratome for soft-tissue sectioning, multiheaded light microscope with projection capabilities, system for laser capture microdissection, and slide scanner with analysis software for identification and quantification of morphological structures.Offers expertise in histopathological and immunocytochemial methods, including fixation, dehydration, embedding, sectioning, histological staining, immunolabeling, high-resolution imaging, and quantitative image analysis. Services in sample preparation, offers assistance in imaging and image analysis and provides consultation for ongoing or future research projects, training program for students and investigators who use centrally available equipment.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Open access core facility available to all TAMU users for Metabolomics service and research. Provides different levels of service from drop-off to collaborative projects.Training for TAMU postdoctoral fellows and students to use instrumentation in support of specific projects.Short courses and workshops on advances in metabolomics. Instrumentation for targeted and untargeted metabolomics analysis.Provides mass spectrometers that are coupled to liquid chromatography (LC) or gas chromatography (GC) separation systems.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Core to facilitate, amplify, and accelerate biological research and discovery through application of bioinformatics. Provides bioinformatic analysis services for Next Generation Sequencing (NGS) data.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Nanowell Cytometry platform is shared resource housed in Flow Cytometry Core that provides Koch Institute and MIT researchers access to Microengraving and SeqWell technologies, developed in Love and Shalek Laboratories at Koch Institute. Microengraving platform enables measurement of multiple traits from individual cells derived from wide array of tissues or cell types, such as immune cells either in their native condition or upon stimulation. Platform allows simultaneous assessment from small or large numbers of cells. Additionally, it is possible to obtain genetic information from individual cells of interest. Platform has been employed in projects related to antibody discovery, tumor profiling from various cancer tissues, and immune cell functions in various allergic, infectious or auto-immune diseases.Core offers access to CellCelector, tool which enables users to isolate single cells using ultra-precise robotic micromanipulator. Offers access to nanowell microplates which enable automated isolation of monoclonal and viable clones. Seq-Well is portable, low-cost platform for massively-parallel single-cell RNA-Seq. Barcoded mRNA capture beads and single cells are sealed in array of subnanoliter wells using semi-permeable membrane, enabling efficient cell lysis and transcript capture.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Core provides central hub to help leverage bioinformatics and data science methods in research projects. Services include Transcriptomics: bulk RNA-Seq, single-cell RNA-Seq, and spatial RNA-Seq; Genomics: SNP, structural variants (SV), and copy number variation (CNV) analyses; Regulatory genomics: ChIP-Seq, ATAC-Seq, CUT&RUN, and Hi-C; Functional genomics: CRISPR-based loss-of-function screens;Image and metadata analysis: AI/ML-based approaches including knowledge graphs. Offers training, education, collaboration, consultation,custom guidance on study design and analysis approaches. Provides classroom and custom training sessions on computational, data science, bioinformatics topics, tailored workshops for requested specialized topics. Offers technical infrastructure and support, computing resource optimization and facilitation, bioinformatics software deployment (conda environments and Docker containers), version control and reproducible science (Git repositories), data management support and submission to public repositories.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Facility offers histological services including Tissue Sectioning:Paraffin embedding and frozen embedding in OCT;Paraffin section serial, random, serial interrupted;Frozen section thaw mount cold/warm, serial, free floating,thick slice, random and serial interrupted, CryoJane tape transfer;Vibratome section;Routine staining, i.e., H+E, Nuclear Fast Red Special staining, Alcian Blue, Cresyl Violet, PAS, Oil Red , Toluidine Blue, Von Kossa, Combined Massons Elastin, Picrosirius Red, Sudan IV, Thionin, Prussian Blue, Movats Pentachrome, Masson Trichrome, Alcian Blue/Phloxine/Tartrazine, others available upon request. Immunohistochemistry/Enzyme:ABC method (direct/indirect);Fluorescence;Biocytin detection;HRP;Single and multiple-labeling;Edu/Brdu,in situ Hybridization,RNAScope,BaseScope.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Core provides technical expertise, training and access to instrumentation, enabling and supporting use of flow cytometry techniques. Allows simultaneous multiparametric analysis of many thousands of cells per second, enabling trained researchers to rapidly analyze complex cell populations using benchtop analysis flow cytometers. High-speed assisted cell sorting services provide researchers with fast, objective and quantitative recording of fluorescent signals from individual cells combined with physical separation of cells of particular interest.Services include High-end, staff assisted cell sorting, using four different high speed sorters;Unassisted bench-top analysis available 24/7;Assisted bench-top analysis available by appointment;Extensive training on bench-top analyzers;Extensive training on FACS Aria sorters;Consultation on experimental design and data interpretation.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Core Facility provides access to Atomic Force Microscope and Leica SP5 Scanning Laser Confocal Microscope, located in Room 122 of Pickus Center for Biomedical Research on Biddeford Campus.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Core provides computational resources and expertise to enhance productivity of researchers studying infectious diseases. Assists with virtual screening, protein-small molecule docking, binding site prediction, protein modeling and design, prediction of protein stability changes upon mutation, fragment based probe design, as well as preparation of presentation graphics.Specializes in initial hit identification of non-traditional drug targets such as protein-protein or protein-RNA interfaces by offering high-throughput virtual screening via pocket optimization with exemplar screening at protein-protein interfaces and hotspot pharmacophore mimicry of protein-RNA interactions.CCB works in collaboration with Molecular Graphics and Modeling Laboratory.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Core provides means to grow thin films of metals and metal oxides. Facility contains two state of art deposition chambers PVD PLD/MBE 2300 and a PVD nanoPLD 1000. PLD provides convenient way to make thin films of materials heretofore studied in bulk by pressing and sintering target from bulk material; facilities are available at Northwestern for pressing and sintering of targets.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Core provides access to advanced chromatographic and mass spectrometry instrumentation. Main analytical focus is quantitative analysis of small molecules (drugs, drug metabololites, endogenous metabolites, xenobiotics and toxicants) and intact large molecules (biologics, intact proteins, and biopolymers like hyaluronan). Provides analytical instruments including Liquid Chromatography and Mass Spectrometry, Microbalances, Quantitative PCR (qPCR or Real-Time PCR), Sample Preparation Aids, Pharmacology Department Shared Instruments.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Core at University of Washington (UW) is managed by Department of Comparative Medicine and open to investigators with research needs to maintain mice free of any microorganisms (germ-free), or with known population of microorganisms (gnotobiotic).Services provided include Rederivation, Germ-Free (GF) Mice, Isolator Maintenance of GF Mice, Experimental Study Support, Diet Sterility Testing, Technical Procedures.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Core provides technical assistance to Brown researchers by performing flow cytometry-based analysis and sorting. Facility has 4-laser, 19-parameter BD FACSAria IIIu for flow and sorting applications, as well as 3-laser, 15-parameter BD FACSCelesta equipped with high throughput system for analysis of samples from 96 well plates.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Core provides access to expertise, training and specialized instrumentation related to tissue processing, sectioning, staining, immunohistochemistry and microscopy. Offers services and training related to image analysis and image analysis software to guide investigators in choosing best methods for presenting their data.Services include Trimming of wet tissues,Tissue processing into paraffin, OCT and paraffin embedding, Sectioning of paraffin-embedded/frozen tissues, Routine and special histochemical staining, Immunohistochemistry/Immunofluorescence, Antibody optimization, Brightfield/ widefield/ confocal microscopy, Image capture and image analysis.Core has cryostats, microtomes and microscopes available for reservation.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth