Curator Dashboard

Facility provides training, consulting, assisted use and independent access for wide variety of cell sorting and analysis.

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• SciCrunch
• 5 years ago - submitted by Edyta Vieth

Software tool fo detecting genomic breakpoints of fusion transcripts in random hexamer RNA-seq data. Used for detection of exonic, intronic and intergenic fusion transcripts and their genomic breakpoints in poly(A)+ and rRNA-minus RNA sequencing data.

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• SciCrunch
• 5 years ago - submitted by Youri Hoogstrate

Core has range of instruments for characterization and structure elucidation of chemical and biophysical samples. Our staff maintains instruments and provides data collection services as well as training and support for self use of many of our instruments. We are most equipped in areas of NMR spectroscopy, Mass spectrometry and X-ray crystallography, but we also have optical and calorimetric instruments.

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• SciCrunch
• 5 years ago - submitted by Edyta Vieth

Core is full service histology laboratory available to faculty, researchers, clinicians and students.Provides histological services for both animal and human tissue. Services include paraffin processing and embedding, paraffin and frozen sectioning as well as routine and special histological staining.Equippemnt includes:Leica Bond III Immunostainer to provide automated immunohistochemistry, in-situ hybridization and immunofluorescence staining;Automated tissue processors for paraffin processing; Automated microtomes for paraffin sectioning; Automated stainer that can be programmed to provide wide variety of routine and special stains;Cryostats for sectioning frozen tissue; Tissue Microarray machine.LPHCF can also perform manual chromogenic or fluorescent staining (single or multi-color labelling) on frozen and paraffin sections. We also provide full service slide scanning using Axio Scan.Z1 for Brightfield or Fluorescent stained slides at either 20X or 40X magnification.Personnel in the LPHCF are available for consultation on project/protocol design, technical assistance and training on facility instruments.Infinity software system is used for all of our histological services and instrument training.

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• SciCrunch
• 5 years ago - submitted by Edyta Vieth

Software as cloud based community driven repository to store, share, and publish traumatic brain injury research data. Aims to increase transparency with individual level data, enhance collaboration, facilitate advanced analytics, and conform to increasing mandates by funders and publishers to make data accessible. Members of ODC-TBI have access to private digital lab space managed by PI or multi-PIs for dataset storage and sharing. PIs can share their labs’ datasets with registered members of ODC-TBI community and make their datasets public and citable. ODC-TBI implements stewardship principles that scientific data be made FAIR (Findable, Accessible, Interoperable and Reusable).

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• dkNET
• 5 years ago - submitted by Jeffrey Grethe

Software Python package.Python analysis module for AVATAR recording system. Uses three-dimentional coordinate data to produce motor coordination data from general information like velocity and total distance to behavior clustering based on python scripts.

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• RRID-Legacy
• 5 years ago - by Anonymous

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• RRID-Legacy
• 5 years ago - by Anonymous

Software tool to profile enrichment of next generation sequencing reads at transposable elements. Method to estimate repetitive element enrichment using high throughput sequencing data. Used to study genome wide transcriptional regulation of repetitive elements.RepEnrich2 is updated method to estimate repetitive element enrichment using high-throughput sequencing data.

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• RRID-Legacy
• 5 years ago - by Anonymous

Software tool as 3D adult zebrafish brain atlas for digital age. Built by combining tissue clearing, light-sheet fluorescence microscopy, and three-dimensional image registration of nuclear and antibody stains.

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• RRID-Legacy
• 5 years ago - by Anonymous

National research program to learn how genes, lifestyle, and military exposures affect health and illness.

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• RRID-Legacy
• 5 years ago - submitted by Anita Bandrowski

Collaborative environment hosting scientists from backgrounds ranging from neuroanatomy, to microscopy and computer science, facilitating production, collection, and analysis of brain wide connectivity data. Home of Mouse Connectome Project seeks to develop multimodal multiscale connectome and cell-type map of mammalian brain using advanced tracing, imaging, and computational methods.Crossdisciplinary group develops neuroanatomic and neuroinformatic approaches to understand connectivity patterns in health and disease. Portal includes iConnectome Viewer, iConnectome Maps and Atlas Viewer.

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• RRID-Legacy
• 5 years ago - submitted by Anita Bandrowski

Core supports genome engineering using CRISPR technology. Provide services to generate knockouts, insertions, deletions, and point mutations in various organisms. Services for genome engineering include guideRNA design, homology-directed repair template design, production of modified mammalian cell lines, preparation of reagents for delivery to embryos, and mutation detection by targeted deep sequencing. Pooled screening is also coordinated and supported by our team.We acquire, prepare, and validate pooled libraries as an Institute resource. In coordination of our pooled screen workflow, we work with other teams to track the progress of these projects. Once resulting cell populations from the screen are delivered, our team does genomic DNA purification, target amplification, and preparation for NGS. We now offer a TAIL-PCR service to identify the location of random integration events. We have successfully identified locations in killifish, fly, zebrafish, and sea anemone.Team is responsible for maintaining and distributing clone and vector collections for the Institute.

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• SciCrunch
• 5 years ago - submitted by Edyta Vieth

Proteomics and Metabolomics services and collaborative efforts are provided at Biological Mass Spectrometry Facility. We use high resolution Orbitrap mass spectrometers with UPLC at high flow for metabolomics and nanoUPLC for proteomics work. We have Bruker Autoflex for self service MALDI. Our proteomics services are protein ID, quantitation, and modification analysis, with fractionation for deeper coverage and de novo sequencing of mAbs available. We collaborate for customized projects. We have untargeted metabolomics for quantitative or qualitative analysis of extracted metabolites using C18 column.

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• SciCrunch
• 5 years ago - submitted by Edyta Vieth

Full Service DNA Sequencing and Genotyping facility. Offers Sanger,Fragment Analysis, Illumina, RT and Digital PCR, Single Cell, large projects, sample/library prep and QC.Houses state of the art instruments for all your sequencing needs including, capillary DNA analysis, single cell applications, long read capabilities. We also provide many instruments that can be operated by you for sample preparation and quality control of all sample types.

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• SciCrunch
• 5 years ago - submitted by Edyta Vieth

Software R package to discover and predict, visualize and analyze mutational signatures. Used to count and combine multiple mutation types, including SBS, DBS, and indels. Calculates replication strand, transcription strand and combinations of these features along with discovery from unique and proprietary genomic feature associated with any mutation type.

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• RRID-Legacy
• 5 years ago - by Anonymous

Software package for ZEISS light microscopy systems. Universal user interface for every imaging system from ZEISS to assist to acquire images, process images, visualize big data by GPU powered 3D engine, analyze images via Machine Learning-based tools, correlate between light-light or light-electron microscopes, store raw data in secure format locally or in the cloud., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• RRID-Legacy
• 5 years ago - submitted by Tomas Ragauskas

Software tool that using machine learning classifiers relies on ensemble of experts in order to provide efficient classification in metagenomic contexts. Used for DNA sequences in metagenomic samples.

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• RRID-Legacy
• 5 years ago - submitted by Alexandre Lourenço

Web server predicts and visualizes mutation induced structure changes of single nucleotide polymorphism in RNA sequence. This covers changes in accessibility (single strandedness) of molecule, its intra molecular base pairing potential and its base pairing probabilities. One of Freiburg RNA tools.

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• RRID-Legacy
• 5 years ago - by Anonymous

Portal provides tools for visualizing, querying, and downloading cancer data, which is released on quarterly schedule.

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• RRID-Legacy
• 5 years ago - by Anonymous

Software tool for analysis of cell and nuclear morphology from fluorescence or bright field images. Enables profiling and classification of cells into shape modes based on equidistant points along cell and nuclear contours. Robust method to quantify cell morphological heterogeneity.

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• RRID-Legacy
• 5 years ago - by Anonymous