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https://med.und.edu/imaging/index.html

Provides advanced instrumentation for researchers interested in investigating biological processes at cellular, sub cellular and molecular level.Instrumentation include Confocal Microscope Systems :Zeiss LSM-510 Meta Confocal Microscope, Olympus FV1000 MPE Basic Multiphoton Microscope;Brightfield/Fluorescence: Nikon Eclipse TE300 (inverted) Fluorescent Microscope, Nikon Eclipse 80i (upright) Fluorescent Microscope, Leica Thunder Imager; TIRF Systems:Olympus TIRF Microscope; Transmission Electron Microscopy:Hitachi 7500 TEM, RCM MTX Ultramicrotomes;Scanning Electron Microscopy:Hitachi 4700 Field Emission SEM, Denton Desk II Sputter and Turbo-sputter Coaters.Light and electron microscopic facilities, complete with ancillary support equipment, are located in close proximity to each other within suite of rooms housed in medical school.

Proper citation: University of North Dakota School of Medicine and Health Sciences Imaging Core Facility (RRID:SCR_017733) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/thornton-srv/databases/profunc/index.html

The ProFunc server had been developed to help identify the likely biochemical function of a protein from its three-dimensional structure. It uses both sequence- and structure-based methods including fold matching, residue conservation, surface cleft analysis, and functional 3D templates, to identify both the protein''''s likely active site and possible homologues in the PDB. Often, where one method fails to provide any functional insight another may be more helpful. You can submit your own structure, analyze an existing PDB entry, or retrieve the results of a previously submitted run. The files are usually stored for about 6 months before being deleted. However, they are stored on a partition that is not backed up; so, in principle, they could disappear at any time.

Proper citation: ProFunc (RRID:SCR_004450) Copy   

•   Source: SciCrunch Registry

http://murphylab.web.cmu.edu/services/SLIF/

SLIF finds fluorescence microscope images in on-line journal articles, and indexes them according to cell line, proteins visualized, and resolution. Images can be accessed via the SLIF Web database. SLIF takes on-line papers and scans them for figures that contain fluorescence microscope images (FMIs). Figures typically contain multiple FMIs, to SLIF must segment these images into individual FMIs. When the FMI images are extracted, annotations for the images (for instance, names of proteins and cell-lines) are also extracted from the accompanying caption text. Protein annotation are also used to link to external databases, such as the Gene Ontology DB. The more detailed process includes: segmentation of images into panels; panel classification, to find FMIs; segmentation of the caption, to find which portions of the caption apply to which panels; text-based entity extraction; matching of extracted entities to database entries; extraction of panel labels from text and figures; and alignment of the text segments to the panels. Extracted FMIs are processed to find subcellular location features (SLFs), and the resulting analyzed, annotated figures are stored in a database, which is accessible via SQL queries.

Proper citation: Subcellular Location Image Finder (RRID:SCR_006723) Copy   

•   Source: SciCrunch Registry

http://www.uwyo.edu/microscopy/

Core to assist researchers and students in their imaging needs of fluorescence and electron microscopy and to increase use of microscopes in science education. Consultation, training or touring facility is also available by appointment.

Proper citation: Wyoming University Jenkins Microscopy Core Facility (RRID:SCR_017758) Copy   

•   Source: SciCrunch Registry

https://www.unr.edu/proteomics

Core offers mass spectral proteomic analysis. Assists with qualitative and quantitative characterization of proteins in biological matrices such as plasma/serum, tissue, cell lines and other biological material to gain understanding of physiological pathways, molecular interactions and regulatory signaling.

Proper citation: University of Nevada at Reno Nevada Proteomics Center Core Facility (RRID:SCR_017761) Copy   

•   Source: SciCrunch Registry

http://bioimaging.dbi.udel.edu

Microscopy facility that houses equipment including confocal microscopes: LSM780 confocal microscope (Located at CBBI),LSM880 confocal microscope (Located at DBI 117),electron microscopes and their accessory instrumentation:Thermo Scientific Apreo VS SEM microscope,Hitachi S-4700, Leica EM ACE600 and Tousimis Autosamdri-815B,CX7 high content analysis system. Our staff has technical expertise across different microscopy platforms and methodologies.

Proper citation: University of Delaware BioImaging Center Core Facility (RRID:SCR_017814) Copy   

•   Source: SciCrunch Registry

https://www.une.edu/research/cobre/histology

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.

Proper citation: University of New England COBRE Histology and Imaging Core Facility (RRID:SCR_017885) Copy   

•   Source: SciCrunch Registry

http://proteomics.northwestern.edu/collaborate

Core offers multiple types of experiments from simple protein identification to protein quantitation. Performs traditional bottom-up proteomics, where proteins are digested with enzyme prior to analysis and intact, top-down proteomics analyses. Services include proteins identification after in-gel or in-solution digestion, top-down mass spectrometry to preserve post-translationally modified forms of proteins present in vivo by measuring them intact, IP-MS Pulldown,BioID service to identify target of biotin ligase that has been tagged onto their protein via traditional cloning methods,Untargeted Quantitative Peptide Proteomics,Targeted Quantitative Peptide Proteomics,Epiproteomic Histone Modification Panel A,Epiproteomic Histone Modification Panel B,Untargeted Metabolomics,Phosphoproteomics,PTM Scan,ChIP-MS.

Proper citation: Northwestern University Proteomics Core Facility (RRID:SCR_017945) Copy   

•   Source: SciCrunch Registry

https://lmf.mdibl.org/

Core provides professional scientific expertise in light microscopy. Offers access to hardware and software as well as expert guidance at any step of imaging project, from experimental design to image analysis.Comprises eight microscope systems including two laser scanning confocal microscopes including one Olympus inverted confocal microscope system (FV1000) and one Zeiss inverted confocal microscope system (LSM-980) equipped with Airy scan 2 for super resolution and 2-photon technology for in-vivo deep imaging with temperature controlled chamber. One spinning disk confocal including Nikon inverted spinning disk microscope system with incubation chamber (Eclipse Ti with Yokogawa disk CSU-W1), two Zeiss widefield microscopes for brightfield and epifluorescence illumination (Zeiss Apotome and Zeiss Colibri), three macroscopes systems to observe large samples or complete model organisms in brightfield and epifluorescence including one Olympus stereomicroscope system (MVX10) and two Zeiss stereomicroscope systems (SteREO Discovery V12), fully automated and one AxioZoom V16 , fully automated with ApoTome attachment.

Proper citation: Mount Desert Island Biological Laboratory Light Microscopy Core Facility (RRID:SCR_019166) Copy   

•   Source: SciCrunch Registry

https://jcesom.marshall.edu/research/office-of-research-and-graduate-education/core-facilities/genomics/

Core provides services including high throughput next generation sequencing (NGS) to support whole genome, whole exome, RNA-Seq, single cell RNA-Seq, microbiome and global chromatin and methylation studies, biostatistical and bioinformatic support for NGS projects, access to DNA/RNA sequence analysis software, automated Sanger DNA sequencing, genotyping and RNA/DNA quality assessment, access to shared instrumentation such as plate readers, real time thermal cyclers, Agilent Bioanalyzers, fluorimeters, and spectrophotometers.

Proper citation: Marshall University School of Medicine Genomics Core Facility (RRID:SCR_018885) Copy   

•   Source: SciCrunch Registry

https://cancer.dartmouth.edu/scientists-researchers/molecular-biology-resource

Genomics Section provides services and instrumentation that enable DNA/RNA extraction and quality control, next-generation Illumina and Nanopore sequencing, epigenetic profiling, and microarray analysis on a whole-genome scale, from the level organisms to single cells. Molecular Biology Section provides DNA fragment analysis qPCR, Sanger sequencing and NanoString Technology.

Proper citation: Dartmouth Genomics and Molecular Biology Shared Resource (GMBSR) (RRID:SCR_021293) Copy   

•   Source: SciCrunch Registry

http://www.med.uvm.edu/vigr/home

Core provides services for Experimental Design, Metagenomics, Comparative Expression Analyses, Variant Analyses, and Systems Biology. Overarching umbrella encompassing four distinct shared resource facility arms: DNA Analysis,Microarray,Massively Parallel Sequencing Facilities,Bioinformatics Shared Resource.

Proper citation: University of Vermont Integrative Genomics Resource Core Facility (RRID:SCR_021775) Copy   

•   Source: SciCrunch Registry

https://polymerscreen.yale.edu

Open access web app that allows users to search for optimal condition for extraction of membrane proteins into membrane active polymers which allows for retention of native membrane environment around target protein.

Proper citation: MAP Database Guide for Membrane Protein Solubilization (RRID:SCR_025656) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/SpaGCN/

Software graph convolutional network to integrate gene expression and histology to identify spatial domains and spatially variable genes. SpaGCN integrates information from gene.

Proper citation: SpaGCN (RRID:SCR_025978) Copy   

•   Source: SciCrunch Registry

https://github.com/zhouhj1994/LinDA

Software linear models for differential abundance analysis of microbiome compositional data. Used to tackle compositional effects in differential abundance analysis. It fits linear regression models on centered log2-ratio transformed data, identifies bias term due to transformation and compositional effect, and corrects bias using mode of regression coefficients. It could fit mixed-effect models.

Proper citation: LinDA (RRID:SCR_025966) Copy   

•   Source: SciCrunch Registry

https://github.com/YingMa0107/CARD/

Software R package for spatial transcriptomics. Deconvolution method that combines cell-type-specific expression information from single-cell RNA sequencing (scRNA-seq) with correlation in cell-type composition across tissue locations.

Proper citation: Conditional AutoRegressive Deconvolution (RRID:SCR_026310) Copy   

•   Source: SciCrunch Registry

https://endomap.hms.harvard.edu/

Structural interactome viewer. Interactive database of endosomal protein-protein interactions identified by cross-linking mass spectrometry and modeled by AlphaFold multimer. Structural protein interactome of human early endosomes.

Proper citation: EndoMap (RRID:SCR_026690) Copy   

•   Source: SciCrunch Registry

https://github.com/compgenomics/MeTPeak

Software package for finding the location of m6A sites in MeRIP-seq data.

Proper citation: MeTPeak (RRID:SCR_026533) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://bioams.llnl.gov/

Biomedical technology research center that develops and refines accelerator mass spectrometry methods and instrumentation for the precise, quantitative and cost-effective measurement of the effects of drugs and toxicants on humans at safe doses. It facilitates the use of accelerator mass spectrometry in biomedical research and provides training and access for researchers.

Proper citation: National Resource for Biomedical Accelerator Mass Spectrometry (RRID:SCR_009006) Copy   

•   Source: SciCrunch Registry