The Emory Integrated Core Facilities (EICF) provide a number of facilities for use by all investigators in the state of Georgia.  Specific core services include cellular imaging and systems imaging, biostatistics and bioinformatics, electron microscopy, a personalized immunotherapy center, flow cytometry, genomics, proteomics, transgenic mouse and gene targeting, and rodent behavioral characterization.

http://www.cores.emory.edu/

The Emory Biostatistics Collaboration Core (BCC) provides state-of-the-art statistical and bioinformatics analysis. Our mission is to collaborate with investigators to choose appropriate study designs for quantitative analysis and to assure appropriate implementation of statistical methodology in research. BCC personnel are available for discussion at all stages of research, including initial study planning, preparation of grants and contracts, database design and management, analysis of existing datasets, assistance in preparing statistical content for manuscripts and presentations and statistical review of manuscripts in the publication process. The BCC has access to a broad range of computer hardware and software and personnel with expertise in using major statistical, graphics, and data management packages.

The Biostatistics Collaboration Core (BCC) is subsidized by the Emory University School of Medicine with is one of the Emory Integrated Core Facilities. Additional support is provided by the Georgia Clinical & Translational Science Alliance of the National Institutes of Health under Award Number UL1TR002378.

The Center for Systems Imaging Core (CSIC) is a cross-disciplinary scientific, administrative, and educational home for imaging science at Emory University. The mission of CSIC is to help investigators in the Emory and Greater Georgia research community utilize state-of-art human and animal imaging technologies in their research. CSIC also supports the advancement of scientific research focused on the development of imaging biomarkers and serves to build interdisciplinary educational symposia and training programs.

The major imaging equipment housed at CSIC include a State licensed radiochemistry lab, a 11MeV Eclipse cyclotron, three 3T MRI Prisma scanners and one 3T MRI Skyra scanner, a PET/MRI (3T) scanner, a HRRT human brain PET system, a XCT 2000 (qCT) scanner, an Inveon micro PET-CT system, and a small animal imaging 9.4T MRI scanner.

The Emory Glycomics and Molecular Interactions Core provides provides investigators with the tools and expertise needed to use rapidly evolving methods and technologies in the area of glycomics. 

TheEmory Glycomics and Molecular Interactions Core provides state-of-the-art molecular interaction assay technologies and using surface plasmon resonance with a BiaCore X100, isothermal titration calorimetry with a MicroCAiAuto-iTC200, and glycan microarray analyses using a variety of glycan microarrays comprised of various classes of glycans.

The Emory Glycomics and Molecular Interactions Core is subsidized by the Emory University School of Medicine and is one of the Emory Integrated Core Facilities. Additional support is provided by the National Center for Advancing Translational Sciences of the National Institutes of Health under Award Number UL1TR000454. 

The Emory Flow Cytometry Core (EFCC) is a full-service flow cytometry facility offering Emory researchers the ability to use the latest sorters and analyzers in their research.

The Emory University School of Medicine Flow Cytometry Core (EFCC) provides state-of-the-art high-speed sorting, sample analysis and analyzer training facilities. Mission priority #1 is to provide the highest customer satisfaction to our clients. This Flow Cytometry Core Facility provides quantitative flow cytometric analyses on samples from a wide variety of biological matrices, e.g. blood, bone marrow, spleen, serum, plasma, solid tissues, cell extracts, etc., to support both clinical and basic research efforts on the campus and the surrounding area.

The Emory Flow Cytometry Core (EFCC) is one of the Emory Integrated Core Facilities (EICF) and is subsidized by the Emory University School of Medicine. Additional support is provided by the National Center for Georgia Clinical & Translational Science Alliance of the National Institutes of Health under Award Number UL1TR002378.

The Emory Integrated Computational Core (EICC) mission is to provide cutting-edge computational support and bioinformatics analysis to Emory researchers and users of users of other Emory Integrated Core Facilities. In effect, we act as the "digital hub" for all the Emory Integrated Core Facilities. 

The Emory Integrated Computational Core (EICC) is subsidized by the Emory University School of Medicine and is one of the Emory Integrated Core Facilities. Additional support is provided by the National Center for Georgia Clinical & Translational Science Alliance of the National Institutes of Health under Award Number UL1TR002378. 

Emory Integrated Genomics Core

The Emory Integrated Genomics Core (EIGC) provides investigators with the tools and expertise needed to use the latest genomics technologies in their research.

The Emory Integrated Genomics Core’s (EIGC) central mission is to help Emory investigators effectively use state-of-the-art genomics platforms in pursuit of their research goals. Our primary platforms use next-generation sequencing technologies to characterize genomes in order to use these data as tools of discovery. Services include whole genome/exome sequencing, RNA-seq and preparation/sequencing of other epigenetic libraries (DNA methylation, ATAC-seq, ChIP-seq), single cell RNA-seq and ATAC-seq, Nanostring nCounter transcriptome profiling, spatial profiling, structural variation detection, and 16S rDNA amplification and sequencing for microbiome studies. The EIGC also maintains CLIA certification, offering assay validation and nucleic acid extraction services from a wide variety of biological sources, including blood, serum, plasma, solid tissues, cell extracts, etc., to support both basic research and clinical efforts on campus. We can also help characterize and confirm the identify of cell lines, which is critical for scientific rigor and reproducibility.

The Emory Integrated Genomics Core (EIGC) is subsidized by the Emory University School of Medicine and is one of the Emory Integrated Core Facilities. Additional support is provided by the Georgia Clinical & Translational Science Alliance of the National Institutes of Health under Award Number UL1TR002378.

*** For cancer-related research supported by the Winship Cancer Institute ONLY:

Partial support is providedby the Emory Integrated Genomics Core (EIGC) Shared Resource of Winship Cancer Institute of Emory University and NIH/NCI under award number P30CA138292.

FACILITIES & OTHER RESOURCES

Updated: April 2023

Fields Relevant for the Emory Integrated Genomics Core (EIGC)

Other:

The Emory Integrated Genomics Core (EIGC), one of the Emory Integrated Core Facilities (EICF), consists of three service categories which provide unique services to Emory clinical and basic researchers. The central mission of the EIGC is to provide a top-tier genomics resource that is widely available to the Emory research community and that integrates cutting-edge genomics technologies with downstream analyses. The EIGC’s Clinical Laboratory Improvement Amendments (CLIA) Services (CLIA: 11D1086150) provide nucleic acid isolation and QC services and cell line validation. The CLIA services provide support for clinical trials research using genomics technologies that need to be conducted in a CLIA certified environment with CLIA validated protocols. Aliquots of human samples isolated in the EIGC can also be transferred to other CLIA/CAP certified testing facilities for clinical diagnostic testing. The EIGC’s Genomics Research Services provide a wide variety of genomics services which include genotyping assays like the Infinium Methylation EPIC array and TaqMan Genotyping assays; library preparation for 16S rDNA microbiome, targeted sequencing (Fluidigm Access Array), single cell sequencing (10X Genomics), RNAseq, ATACseq, and reduced representation bisulfite sequencing; Illumina-based Next-Generation sequencing using the Illumina MiSeq and NextSeq platforms; transcriptome analysis (Nanostring nCounter); spatial profiling services using Visum (10X Genomics) and GeoMx (Nanostring) platforms; and genome editing validation. The EIGC has adopted an innovative business model whereby large-scale next-generation sequencing is outsourced to other academic and commercial entities, with the ultimate goal of obtaining the lowest cost, highest quality, and fastest turn-around for our customers. The EIGC’s Genome Engineering Services offer custom cloning services for Emory investigators in support of functional genomics applications.

The EIGC staff include four PhD-level scientists, providing expertise on genomics platforms, epigenetics services, cancer biology, CLIA protocol, custom cloning, genome editing, and other support. The lab is supported by 7 additional staff. The Core Director (Dr. Lyra Griffiths) and Scientific Director (Dr. Christopher Scharer) provide project planning and grant application support. Dr. Thomas Schneider ist he EIGC CLIA director. EIGC works closely with the Emory Integrated Computational Core (EICC) and the Biostatistics Shared Resource at Winship Cancer Institute in order to support our investigators with computational support.

The EIGC is located in a CLIA certified laboratory located on the 7th floor of the Woodruff Memorial Research Building, with 2400 square feet of dedicated wet-lab space. The EIGC’s laboratory areas include dedicated pre- and post-PCR spaces. Two chemical fume hoods and a biological safety cabinet are also located within the space. The EIGC is located adjacent to the EICC and common public meeting room space on the 7th floor of the Woodruff Memorial Research Building, allowing for project planning meetings that span both cores and weekly EIGC team meetings. A secondary location is on the 4th floor of the Health Sciences Research Building, with 770 square feet of wet-lab space and contains a bioligical safety cabinet. This secondary location is adjacent to the Emory Flow Cytometry Core, providing the possibility to streamline collaborative projects.

MAJOR EQUIPMENT

Updated: April 2023

Major Equipment for Emory Integrated Genomics Core (EIGC) Users

EMORY INTEGRATED GENOMICS CORE (EIGC)

The Emory Integrated Genomics Core (EIGC), one of the Emory Integrated Core Facilities (EICF), is a CLIA-certified (CLIA:11D1086150) laboratory located on the 7th floor of the Woodruff Memorial Research Building, with 2400 square feet of dedicated wet-lab space. The EIGC’s laboratory areas include dedicated pre- and post-PCR spaces. Two chemical fume hoods and a biosafty cabinet are also located within the space. Additionally, EIGC has a secondary location on the 4th floor of the Health Sciences Research Building, with 770 square feet of wet-lab space including a biosafety cabinet. The EIGC has 500 square feet of dedicated office adjacent to the laboratory space on the 7th floor of the Woodruff Memorial Research Building, which provides for computational services, meeting customers, and weekly EIGC team meetings. The EIGC is composed of three service divisions: CLIA, Genomics Research, and Genome Engineering. Each division provides specialized genomics research services to Emory investigators. A Thermo Scientific Nautilus Laboratory Information Management System (LIMS) is hosted at Emory and all data is stored on-site in a HIPAA secure zone. This LIMS provides the foundation for EIGC workflows and fosters collaboration across the Emory campus and with external consortia. The EIGC closely coordinates with the Emory Integrated Computational Core (EICC), which is located on the 7th floor of the Woodruff Memorial Research Building adjacent to the EIGC to provide computational and bioinformatics services for Emory investigators. The EIGC infrastructure includes:

DNA/RNA Extraction, Genotyping, and Gene Expression:

10X Genomics Chromium and Chromium X Controllers: An automated system that allows one to encapsulate samples into hundreds to tens of thousands of uniquely addressable partitions in minutes, each containing an identifying barcode for downstream analysis. Supports a wide variety of assays when combined with Illumina sequencing that include: Single Cell Gene Expression, Single Cell Immune Profiling, Single Cell Copy Number Variant Detection, Single Cell ATACseq, Genome sequencing, Exome sequencing, de novo Assembly of genomes.

AirClean PCR Workstation: Provides a clean air environment in order to prevent sample contamination.

Agilent Fragment Analyzer (48/96 wells): A parallel capillary electrophoresis instrument designed to speed nucleic acid fragment analysis and quality control before moving onto downstream applications.

Agilent 2100 Bioanalyzer: Allows for rapid quantification of nucleic and proteomic samples, while providing information about the size distribution of the fragments.

Agilent 2200 TapeStation: Provides simple, fast, and reliable electrophoresis of DNA, RNA, and proteins.

Applied Biosystems SeqStudio Flex: A multi-color fluorescence-based DNA analysis system using the technology of capillary electrophoresis with 8 capillaries operating in parallel. This fully automated system separates amplified fragments of varying sizes for analysis of short tandem repeats (STRs) among individuals and extended pedigrees as well as sequencing.

Applied Biosystems 7900HT: Is a real-time quantitative PCR system that combines 96- and 384-well plate compatibility with fully automated robotic loading. Key applications include gene expression quantitation and the detection of single nucleotide polymorphisms (SNPs) using the fluorogenic 5' nuclease assay.

BioRad QX200 Droplet Digital PCR System: Droplet digital polymerase chain reaction was developed to provide precision quantification of nucleic acid target sequences. ddPCR measures absolute quantities of nucleic acid molecules encapsulated in discrete water-in-oil droplets by measuring the fluorescence generated by binding of gene-specific probes or EvaGreen double-stranded DNA binding dye within each droplet. ddPCR has the ability to detect gene copy number variation, detect rare sequences from tumor cells, measure gene expression levels, and to detect genome edits (HDR and NHEJ).

Covaris E220 Adaptive Focusing Instrument: Employs ultrasonic pulses to uniformly shear nucleic acids, in a multi-sample format with walk away operation. The instrument can also be used to automate lyses of difficult samples (like mouse tail), shear proteins, and form lipid vesicles.

Eppendorf epMotion 5075t: A liquid handling instrument which is compatible with NGS library preparation used for preparation of NGS libraries and bead cleanup.

Fluidigm AccessArray: A liquid handling instrument that is primarily used for targeted enrichment of specified genomic regions for Illumina sequencing.

Invitrogen Countess: A digital cell counter and viability instrument.

Nanopore Gridion: A sequencing device which provides long-read sequencing capabilities for RNA, cDNA, and DNA.

Nanodrop One Spectrophotometer: A UV-Vis Spectrophotomter which quantifies and qualifies DNA, RNA and protein samples from microliter volumes.

nanoString nCounter FLEX: A highly sensitive, enzyme-free, molecular counting platform for determining gene expression or target enrichment across a predefined panel of genomic regions. The EIGC assists investigators with project planning, sample preparation, and coordination of nCounter services across a number of outside providers.

nanoString GeoMx Technology: A high-plex and high-throughput spatial profiling technology which enables researchers to rapidly and quantitatively assess the biological implications of the heterogeneity within tissue samples. The technology allows selection of regions of interest from tissue on a slide and to quantify RNA or protein for the specific region of interest.

Magnetic Particle Processor: A Kingfisher Flex provides for automated extraction of RNA from FFPE tissue in 96-well format and DNA from FFPE tissue, fresh or frozen tissue, blood, blood products, saliva, urine, and cell cultures in 24-well or 96-well format.

Tecan EVO150: Used to perform pre-PCR routine liquid transfers, such as the transfer of nucleic acids from individual vials into the 96-well storage and amplification plates required by downstream applications.

TissueLyser II. Performs tissue homogenization for DNA and RNA isolation.

Tecan Infinite M200 Pro: Quantitates nucleic acids using either PicoGreen or RiboGreen fluorescence protocols.

Qubit: A device which reads fluorescent assays in order to quantify DNA, RNA, and protein.

Nine Thermal Cyclers: Four Applied Biosystems 9700 Peltier-driven thermal cyclers, one MJ BioRad thermal cyclers, one Eppendorf Mastercycler, three BioRad C1000 and one BioRad Tetrad with four 96-well gradient capable blocks.

Non-instrument computers: There are currently two MacBook Pros, two iMacs and thirteen Dell PCs.

Next Generation Sequencing:

One Illumina MiSeq instrument: A fully integrated next generation sequencing platform capable of generating between 540 Mb (~4 hours) up to 8.5 Gb (~39 hours) of raw sequence. Some applications of this platform include targeted sequencing from complex eukaryotic genomes or cancer tumors, microbial whole-genome sequencing, 16S rRNA sequencing for microbiome studies, and sequencing of bisulfite treated DNA for assessing methylation. Samples preparation is rapid and samples can be multiplexed with sequence tags.

One Illumina NextSeq 550 instrument: A fully integrated next generation sequencing platform capable of generating between 16GB to 120GB in instrument runs that range between 11 to 29 hours per experiment. Some applications of this platform include sequencing RNAseq, ATACseq or single cell libraries, targeted sequencing from complex eukaryotic genomes or cancer tumors, microbial whole-genome sequencing, and sequencing of bisulfite treated DNA for assessing methylation. The NextSeq also has array scanning capabilities utilized to read Infinium microarrays, including the Infinium MethylationEPIC array.

Large-Scale Next Generation Sequencing: The EIGC has adopted an innovative business model whereby large-scale next-generation sequencing is outsourced to other academic and commercial entities, with the ultimate goal of obtaining the lowest cost, highest quality, and fastest turn-around for our customers. Academic partners include the Genomic Services Laboratory at HudsonAlpha and genomics core facilities at Yerkes National Primate Research Center, the University of Georgia, Georgia Institute of Technology, and New York University. Commercial companies include: Discovery Life Sciences, Novogene, Omega Bioservices, Genewiz, Akesogen, Otogenetics, and BGI. We have the flexibility to pursue sequencing projects with any outside provider that provides competitive pricing, rapid turn-around time, and high-quality data. In effect, the EIGC acts as a sequencing service broker, whereby we compete companies against each other to obtain the best pricing and service for Emory investigators.

Emory Integrated Proteomics Core

The Emory Integrated Proteomics Core (EIPC) is a full-service proteomics facility offering Emory researchers the ability to use the cutting-edge mass spectrometry (MS) technologies to identify and characterize proteins in their research. Our major services include a) protein identification (in-gel or in-solution digestion), b) interactome analysis (on-bead digestion), c) post-translational modifications (PTM), d) isobaric (TMT) or label-free quantification, and e) bioinformatic analysis support.

The proteomic platform of EIPC relies on LC-MS/MS to analyze peptide mixtures of single proteins as well as more complex proteomes captured from cells and tissues. The sensitivity and high throughput of the LC-MS/MS system is pivotal to proteomic analyses. Instruments that are currently available in EIPC include Q-Exactive (QE) Plus, Q-Exactive (QE) HF-X, and Orbitrap Fusion.

The Emory Integrated Proteomics Core (EIPC) is subsidized by the Emory University School of Medicine and is one of the Emory Integrated Core Facilities. Additional support is provided by the Georgia Clinical & Translational Science Alliance of the National Institutes of Health under Award Number UL1TR002378.

*** For cancer-related research supported by the Winship Cancer Institute ONLY:

Partial support is provided by the Emory Integrated Proteomics Core (EIPC), Shared Resource of Winship Cancer Institute of Emory University and NIH/NCI under award number 2P30CA138292-04.

The Emory Integrated Metabolomics and Lipidomics Core (EILMC) Facility will provide quantitative lipidomics analyses on lipid samples from a wide variety of biological matrices, e.g. blood, serum, plasma, solid tissues, cell extracts, etc., to support both clinical and basic research efforts on campus. These analyses will provide insight on lipids and lipid precursors whose abundance can be monitored as biomarkers to predict and follow progression of a wide range of diseases. 

The Emory Integrated Metabolomics and Lipidomics Core (EILMC) is subsidized by the Emory University School of Medicine and is one of the Emory Integrated Core Facilities. Additional support is provided by the Georgia Clinical & Translational Science Alliance of the National Institutes of Health under Award Number UL1TR002378.

The Integrated Cellular Imaging Core (ICIC) provides state-of-the-art light microscopy and image analysis technology. We offer confocal and live cell imaging, multi-photon animal and tissue imaging, widefield with deconvolution, super resolution, and image analysis. To effectively implement these technologies, we provide consultations, expert training, and support for all our systems. Along with providing access to equipment, another goal of ICI is to serve as a nucleator for the cell imaging community at Emory. We want to unite diverse microscopy interests, allowing investigators to share ideas, expertise, and instrumentation. Developing new imaging techniques and acquiring new cutting-edge equipment are central to our mission.

*** For pediatrics-related research
Although this is officially an Emory Integrated facility operated out of the School of Medicine, there is a Pediatrics satellite located conveniently on the ground floor in HSRB. Moreover, child health researchers using equipment at any of the ICI locations receive a generous subsidy off regular pricing.

*** For cancer-related research supported by the Winship Cancer Institute ONLY
Partial support is provided by the Emory University Integrated Cellular Imaging Microscopy Core of the Winship Cancer Institute of Emory University and NIH/NCI under award number, 2P30CA138292-04. 

*** For pediatrics-related supported by Emory+Children's Pediatric Research Center ONLY
Partial support is provided by the Emory University Integrated Cellular Imaging Microscopy Core of the Emory+Children's Pediatric Research Center. 

*** For all other research
Partial support is provided by the Emory University Integrated Cellular Imaging Microscopy Core. 

*** For Lattice light sheet microscope research
Partial support is provided by PHS Grant UL1TR000454 from the Clinical and Translational Science Award Program, National Institutes of Health, National Center for Advancing Translational Sciences. 

MOUSE TRANSGENIC AND GENE TARGETING CORE (TMF)

The Mouse Transgenic and Gene Targeting Core (TMF), one of the Emory Integrated Core Facilities (EICF), provides state of the art equipment and expertise for making genetically engineered mouse models, moving alleles on or off-campus, or cryopreserving existing strains of mice. The TMF is located on the ground floor of Emory Health Sciences Research Building and occupies laboratories EG41 and EG42. The EG42 space includes a fully equipped tissue culture suite dedicated to embryonic stem (ES) cell culture, embryology laboratory, microinjection/embryo manipulation space, and surgical suite. The EG41 room includes molecular biology space and cryopreserved embryo/sperm archival space. The TMF has 100 sq ft of dedicated office on the 1st floor of the Health Sciences Research Building, which provides for meeting customers, and TMF team meetings. A dedicated workspace for TMF staff is also located in the HSRB animal facility. The TMF lab is supported by 3 staff members. The Core Director (Dr. Karolina Nitsche) and Scientific Director (Dr. Tamara Caspary) provide grant application support and project consultation.

The animal holding/breeding room is located in EG57 is part of the animal facility and is operated by the Division of Animal Resources (DAR) as detailed below. All the mice used by the core are housed in this facility. It is managed by the Emory University Division of Animal Resources (DAR) in strict compliance with the standards and policies of the Public Health Service. Mice are housed in ventilated auto-water caging system and are changed under laminar flow hoods. The DAR staff is responsible for daily care of the animals as well as health monitoring and surveillance. The DAR also maintains vigorous quarantine and sentinel programs.

The core facility is fully equipped to perform all experimental procedures associated with the production of genetically modified mice. In addition, the core facility has research space and equipment to assist laboratories with auxiliary procedures for the production and analysis of genetically modified mice. These include rederivation and cryopreservation services, and custom mouse needs. The TMF has now several services available  in rat including sperm and embryo cryopreservation and semen evaluation.

The Mouse Transgenic and Gene Targeting Core is subsidized by the Emory University School of Medicine. Additional support is provided by the National Center for Advancing Translational Sciences of the National Institutes of Health under Award Number UL1TR000454.

The Robert P. Apkarian Integrated Electron Microscopy Core (IEMC) at Emory University provides electron microscopy (EM) training and services to academic, clinical, and industry users. The IEMC is located at two sites on the Emory University main campus. Cherry L. Emerson Hall site provides services and training that include conventional (room temperature) transmission electron microscopy (TEM), cryo-transmission electron microscopy (cryo-TEM), cryo-electron tomography (Cryo-ET), conventional scanning electron microscopy (SEM), cryo- scanning electron microscopy (cryo-SEM), energy dispersive spectroscopy (EDS), cryo-electron microscopy of vitrified sections (CEMOVIS), and micro electron diffraction (micro-ED). The Biochemistry Connector site provides services and training in TEM, and single particle cryo transmission electron microscopy (sp-cryo-TEM). Instrumentation at Emory includes a ThermoFisher Talos Arctica 200 kV field emission TEM, a JEOL JEM-2200FS 200 kV field emission TEM (equipped with an in-column Omega filter, hole-free phase-plates, a Direct Electron DE-20, and a Gatan K2 direct electron detectors), a ThermoFisher Talos 120 kV TEM, a JEOL JEM-1400 120 kV TEM, a Hitachi HT7700 120 kV TEM, two field emission SEMs (both capable of cryo-SEM), and a Leica DM6 FS (with STP8000) cryo-CLEM microscope. Additional sample preparation equipment includes two ThermoFisher Vitrobot Mark IV(one on each IEMC site), a Gatan CP3, several plasma-cleaners and glow dischargers, carbon/gold evaporators and sputter coaters, three ultramicrotomes, a Leica UC6i/FC6 cryo-ultramicrotome, a Baltec HPM-010 high-pressure freezer, and a Leica EM AFS2 instrument for freeze substitution and progressive lowering of temperature ( PLT ) techniques.

We have dedicated GPU and CPU clusters, and workstations for image processing, cryo-TEM and cryo-ET data reconstruction and refinement, and data storage.

The Robert P. Apkarian Integrated Electron Microscopy Core (IEMC) at Emory University is subsidized by the School of Medicine and Emory College of Arts and Sciences. Additional support is provided by the Georgia Clinical & Translational Science Alliance of the National Institutes of Health under award number UL1TR000454.

Data can be gathered on the TALOS L 120C TEM, the TALOS Arctica 200kV TEM.

Data can be collected on the JEOL JEM-1400, 120kV TEM, supported by the National Institutes of Health Grant S10 RR025679.

Data can be collected on the JEOL JEM-2200FS 200kV TEM supported by the National Science Foundation Major Research Instrumentation Grant 0923395.

Data can be gathered on the Hitachi HT7700 120kV TEM supported by the Georgia Clinical and Translational Science Alliance under award number UL1TR002378.

The Emory University Rodent Behavioral Core (RBC) plans, executes, and analyzes behavioral experiments examining activity, arousal, coordinated movement, learning and memory, anxiety, depression, seizure susceptibility, reward/reinforcement, and aggression in mice and rats.

The Rodent Behavioral Core (RBC) is subsidized by the Emory University School of Medicine and is one of the Emory Integrated Core Facilities. Additional support is provided by the Emory Neuroscience NINDS Core Facilities (P30NS055077). Further support was provided by the Georgia Clinical & Translational Science Alliance of the National Institutes of Health under Award Number UL1TR002378.

The Emory Personalized Immunotherapy Core is located within the premises of Emory University Hospital Blood Bank. The core is a 300 ft2 clinical-grade, fully equipped, high sterility isolation facility. It is designed as an enabling infrastructure to support early phase clinical trials of cell-based therapies where processing of human cell and tissue is required as part of a FDA-sponsored biopharmaceutical study. It is accredited by the Foundation for the Accreditation of Cellular Therapy (FACT) for more than minimally manipulated cellular therapy products. The facility is manned by a team of highly qualified personnel dedicated to the successful implementation and prosecution of cellular therapy clinical trials. The purpose of this designated Core facility is to directly support investigator-driven phase I/II cell therapy clinical trials at Emory. As a Core facility, EPIC provides a unique resource to the Emory community in assisting the translation of cellular therapies from the bench side to the clinic. The facility possesses the necessary infrastructure to manufacture cellular therapies under FDA approved good manufacturing practices (FDA cGMP Phase I guidance July 2008). This facility was designed to be nimble and adaptable and can support the manufacturing needs of most small enabling cell therapy clinical trials.

The Emory Personalized Immunotherapy Core (EPIC) is subsidized by the Emory University School of Medicine and is one of the Emory Integrated Core Facilities. Additional support is provided by the National Center for Georgia Clinical & Translational Science Alliance of the National Institutes of Health under Award Number UL1TR002378.

The Emory Multiplexed Immunoassay Core (EMIC) help investigators use the latest multiplexed immunoassays in their research. We perform, analyze, and interpret multiplexed immunoassays to measure protein levels in biological matrices (plasma, serum, cerebrospinal fluid, milk, urine, stool, vaginal swabs, tissues, etc.) on the Meso Scale Discovery (MSD) platform.

The Emory Multiplexed Immunoassay Core (EMIC) is subsidized by the Emory University School of Medicine and is one of the Emory Integrated Core Facilities. Additional support is provided by the National Center for Georgia Clinical & Translational Science Alliance of the National Institutes of Health under Award Number UL1TR002378.

The Emory Gnotobiotic Animal Core (EGAC) is the newest member of the Emory Integrated Core Facilities. This cutting-edge core facility offers investigators the opportunity to experimentally manipulate the microbiomes of mice in a controlled environment to gain insight into important biological mechanisms. The EGAC contains a number of 3’ foot wide rigid isolators (Parkbio), each with the capacity to house 12 mice cages each. In addition, the facility has a Tecniplast ISOcageP Bioexclusion system. These are airtight individual mouse cages with high positive pressure that are specifically designed for cage-scale germ-free, gnotobiotic, and bioexclusion studies.

The Emory Gnotobiotic Animal Core (EGAC) is subsidized by the Emory University School of Medicine and is one of the Emory Integrated Core Facilities. Additional support is provided by the Georgia Clinical & Translational Science Alliance of the National Institutes of Health under Award Number UL1TR002378.

The Emory Stem Cell Core (ESCC) is one of the newest members of the Emory Integrated Core Facilities (EICF). The ESCC brings a powerful new research platform in support of Emory investigators. This core’s focus and technical expertise will be to derive and characterize human induced pluripotent stem cells (iPSCs) from terminally differentiated somatic cells using non-integrating methods. Additionally, the core will provide training and educational resources to support investigators with interest in human stem cells. Patient-derived induced pluripotent stem cells (iPSCs) have multiple applications in modeling diseases, drug discovery and screening, toxicological studies and cell therapy, paving the way towards personalized medicine. Emory Stem Cell core provides important support to investigators in Emory University, state of Georgia and beyond. Our services include:

· Somatic cells reprogramming to iPSCs

· Differentiation of iPSCs to various cell types (2D or 3D cell culture)

· Genome editing in human iPSCs (in collaboration with EIGC)

Additionally, the core will provide training and educational resources to support investigators with an interest in human stem cells. 

Emory Stem Cell Core (ESCC) is subsidized by the Emory University School of Medicine and is one of the Emory Integrated Core Facilities. Additional support is provided by the National Center for Georgia Clinical & Translational Science Alliance of the National Institutes of Health under Award Number UL1TR002378".

The Investigational Drug Services Core (IDS) provides investigational drug services to the Winship Cancer Institute in Building C, the Emory Clinic, Buildings A and B, Executive Park, Emory Genetics and the Emory Children's Center.  IDS has two satellite locations at Emory Hospital and The Hope Clinic of Emory University.  The hospital satellite provides services to Emory University Hospitals, the Transplant Clinic and Woodruff Memorial Building.  The Hope Clinic satellite provides pharmacy services to the Hope Clinic, the clinical arm of the Emory Vaccine Research Center (EVC) and a Clinical Core for the Emory Center for AIDS Research (CFAR).

The Emory High Performance Liquid Chromatography Bioanalytical Core (HPLC), one of the Emory Integrated Core Facilities (EICF) measures monoamine neurotransmitters, amino acids neurotransmitters and purines using HPLC methods to support research efforts within and outside of Emory.

The Emory HPLC Bioanalytical Core (EHBC), one of the Emory Integrated Core Facilities (EICF), is supported by the Department of Pharmacology, Emory University School of Medicine and the Georgia Clinical & Translational Science Alliance of the National Institutes of Health under Award Number UL1TR002378.

The Translational Neuroscience Core (TNC) is available for users in the community (Emory, Primate Center, GA Tech, Morehouse, GSU), as well as external users (from academia and industry). The TNC surgical team is unique in performing highly specialized procedures in the brain, spinal cord, and peripheral nerves. These procedures are often necessary to advance preclinical research in the fields of Gene and Stem Cell Therapy, Nerve Repair, Neuromodulation, Chronic Pain, etc. The TNC also assists in building and executing training programs for surgeons (a mandatory FDA requirement prior to clinical application of new techniques and surgical procedures).

FACILITIES AND RESOURCES

Updated 1 July 2022

Fields Relevant for the Center for Systems Imaging Core (CSIC)

CENTER FOR SYSTEMS IMAGING CORE (CSIC)

The Center for Systems Imaging Core (CSIC), one of the Emory Integrated Core Facilities (EICF), provides state-of-the art research and pre-clinical human and animal imaging to the Emory community. The CSIC supports the Center for Systems Imaging (CSI), which is the cross-disciplinary scientific, administrative, and educational home for imaging science at Emory University. The goals of this center are to: (1) support the advancement of scientific research focused on the development of imaging biomarkers, (2) promote the development and application of biomedical imaging technology particularly magnetic resonance imaging, (3) provide core services for human and animal imaging studies, and (4) to build cross-cutting educational and training programs.

The CSIC is housed in approximately 20,200 square feet across the Emory campus. This total comprises a 17,000 square foot facility on the 2nd floor of the Wesley Woods Health Center (WWHC) Building, 800 square feet for human MRI equipment in Emory University Hospital (EUH), 400 square feet for animal MRI equipment in Whitehead Biomedical Research Building (WBRB), and 2,000 square feet jointed MRI scanner and lab space in Emory Executive Park Campus Building 12 (EP12). The major imaging equipment housed at WWHC includes a Cyclotron/Radiochemistry lab, an MRI system, a PET HRRT human brain PET system, an Inveon micro PET-CT system, and a XCT 2000 (qCT) scanner. The Director of CSIC is John Oshinski, PhD (jnoshin@emory.edu) and the Medical Director is Jason Allen, MD, PhD (jason.w.allen@emory.edu).  Co-directors are Jon Nye (PET), Shella Keilholtz, PhD (Animal MRI), Deqiang Qiu, PhD (MRI), Mark Goodman, PhD (Radiochemistry). The Center Administrator is Orman Simpson (osimpso@emory.edu).  There are 11 full time staffs including MRI and PET Technologists, Radiopharmacists, and scientist to provide computer, MRI physics, and small animal support services.

Cyclotron and Radiochemistry

CSIC’s radiochemistry lab is directed by Dr. Mark Goodman, PhD and Ron Crowe (a licensed Radiopharmacist).  The lab houses a Siemens RDS 111 multiport, self-shielded, automated cyclotron producing a 11 MeV, 50 µA proton beam. The cyclotron is equipped with targets for the routine production of curie amounts of [18F]fluoride, [18F]fluorine, [11C]carbon dioxide, and [15O]oxygen. The radiochemistry area is a 2,100 square foot cyclotron vault and laboratory which includes four master slave manipulator arm-equipped hot cells, five mini-cells, one Siemens computer programmable two reaction vessel radiochemical processing unit, one GE TracerLab FXN unit, one semi-automated remote mini-syringe pump, two reaction vessel radiochemical processing units, one semi-automated remote mini-syringe pump fluorine-18 radiochemical processing unit, one automated oxygen-15 water synthesis module, one GE PETtrace carbon-11 methyl iodide module, one clean room, hot and cold waste systems and ventilation chemical and radiation monitoring systems. The radiochemistry laboratory is equipped with four pneumatic tube systems located in the four hot cells for rapid delivery of radiopharmaceuticals. The radiochemistry laboratory is fully equipped with a variety of modern analytical instruments which include one Carroll and Ramsey Associates eleven probe radiation detection system, one Waters Alliance radio-HPLC unit that is configured with UV/Vis and IN/US Radiometric detectors and one Waters radio-HPLC units that are configured with UV/Vis, and Bioscan Radiometric detectors, one Raytest radioactivity thin-layer chromatography system, two electrically activated rheodyne HPLC injectors, eight manual rheodyne HPLC injectors and 4 Waters' 515 HPLC pumps, one Bioscan hot cell radiometric detector, one Agilent 6890N radio-gas chromatograph  equipped with a thermal conductivity and flame ionization  detectors, one Oxford sodium iodide detector and well counter/multichannel analyzer, two Capintec 712M dose calibrators with four remote ionization chambers and four remote readouts and four Mettler electronic balances. The radiopharmacy routinely prepares [68Ga]Netspot, [18F]FACBC aka Axumin, [15O]water, [11C]PIB and [18F]T807 for human imaging studies.

Human Magnetic Resonance Imaging (MRI)

CSIC operates three full-time research dedicated Siemens Magnetom Prisma 3T MR scanners, and a shared clinical/research 3T wide-bore Siemens Skyra scanner. With multiple human research 3T MRI scanners, MRI studies can be effectively distributed across the Emory community. Studies that require close proximity to Emory University Hospital (EUH) or studies performed on in-patients can be performed on the scanner located on the ground floor of the hospital (CSI-EUH). Outpatient studies, where convenience of parking and more flexible scheduling is required can be performed at scanner located at the Wesley Woods (WW) campus (CSI-WW). Both scanners have been recently upgraded to the PrismaFIT platform and VE11C software.  Studies which require a wide-bore scanner or have a study population located at the Brain Health Institute (BHI) at Executive Park can use the Prisma scanner located there or the Skyra scanner next door for up to two hours per day (CSI-BHI).

Research Dedicated 3T Prisma MRI Scanners (EUH and WW)

MRI Scanners. Magnetom Prisma whole-body MR systems are equipped with a state-of-the art gradient system with a maximum (per axis) strength of 80 mT/m and slew rate of 200 T/m/sec, 64 independent RF receiver channels capable of 204 receiver connections, and a 2-channel RF transmitter. Multiple coils are available, including a 64-channel head/neck coil with 52 channels for imaging of the head region, a 32-channel head-only coil, a 20-channel head/neck coil, spine array coil, flexible chest coil, large and small flexible coil for extremity imaging, Tx/Rx CP Head Coil for large no-cap head space, and a 31P dual-tune flexible coil (only for Prisma@EUH) for phosphor spectroscopy. All scanners are running the VE11C version of the Siemens Syngo software. In addition, the scanners are equipped with DirectRF and DirectConnect technology, providing a significant increase in signal-to-noise ratio. The Prisma scanner platform allows efficient acquisition of high-resolution fMRI and DTI images with protocols compatible to those released by the Human Connectome Project. Furthermore, the Prisma scanner located at EUH is equipped with multinuclei spectroscopy and additional shimming power for improved magnetic resonance spectroscopy. A number of advanced research sequences are also available, including Vessel Size Imaging, quantitative Arterial Spin Labeling, Diffusion Spectrum Imaging (for High Angular Resolution Diffusion Imaging) and Simultaneous Multi-Slice EPI (allowing for sub-second high-resolution whole-brain fMRI data acquisition), 4D phase contrast MR for measuring time-resolved flow velocity, displacement encoding with stimulate echoes (DENSE), and multi-echo and ultra-short echo time sequences. With our master research agreement with the vendor, advanced work-in-progress MR sequences from the vendor, collaborators from other institutions, or developed sequences locally can be deployed.

Stimulus and response system for functional MRI. All scanners are equipped with peripheral systems for fMRI. Stimulus/response controls for behavioral tasks concurrent with fMRI are supported by an array of hardware specifically designed to allow investigator flexibility and precision. Visual presentation at EUH and WWHC sites are provided by a high resolution LCD projection system (1400x1050 SXGA, 4200 lumens, 1300:1 ratio) delivered from the back of the suite onto a custom fit screen mounted within the bore behind the participant’s head. The EP12 sites are equipped with Cambridge Research Systems BOLDScreen MRI compatible LED displays. Audio presentation is provided by an Avotec Silent Scan 3100 that has been calibrated to maintain sound pressure levels that are dependent directly on input (flat frequency response +/- 4dB, 200-4500Hz range). A fiber-optic ergonomic bilateral button response system from Psychology Software Tools exists, as well as a control unit to support custom response shapes (joysticks, steering wheels, wands) from Current Designs. All of the hardware are connected through a single switch that signals TTL trigger pulses and allows connectivity to an investigator’s laptop with non-proprietary connections (USB, 1/8” minijack audio, VGA & DVI). A dedicated stimulus and response monitoring computer running Eprime 2.0 and Presentation stimulus programming software also exists. An OptoAcoustics FOMRI MRI-compatible microphone featuring advanced active noise cancellation technology is available for speech fMRI paradigms. CSI-EUH MR scanner is also equipped with multi-nuclei option.  Currently a 31P/1H dual tune flexible coil is equipped and is applicable to phosphor MRS and metabolism studies.

CSI-WW: Other Equipment. A Biopac MP150 (Goleta, CA) MRI-compatible physiological response measurement system is available for collecting peripheral physiological measures. The MP150 system provides high resolution (16 bit), variable sample rates for analog and calculation channels, 16 analog inputs and two analog outputs, digital I/O lines (automatically control other TTL level equipment), and 16 online calculation channels. The MP150 System provides high-speed acquisition (400 kHz aggregate) via an Ethernet connection to a host computer. AcqKnowledge, the Biopac control and analysis software package is used to control the acquisition and can be used for data analysis. Available physiological measures are cardiac pulse, heart rate, heart period, respiratory sinus arrhythmia, respiration and electrodermal activity. The physiological measurements recorded by Biopac can be viewed real-time on a dedicated laptop computer through the Biopac data acquisition software. All responses can be recorded in MatlabTM, text or proprietary Biopac software formats, for retrospective analysis. A MEDRAD (Warrendale, PA) Power Injector system for contrast administration is also available.

CSI-WW: Mock MRI Scanner. A mock MR scanner is set up in the Wesley woods facility. This mock scanner is similar in appearance to the Siemens MRI scanners. It provides stimulus presentation and scanner noise emulations and is used to familiarize pediatric subjects with MRI scanner operation and to acclimate them to the MR scanning environment.

CSI-EUH: Other Equipment. Peripheral equipment, including computers and software for paradigm generation, setup for stimulus presentation, devices for recording behavioral data and physiological parameters including heartbeat, respiration, blood pressure, eye movement, ECG, EEG, and EMG are also established for operation concurrent with MR acquisition. Stimulus generation and presentation setup allows us to present acoustic, electric, and vibrational stimuli and oral and venous administration of liquids. Setup for response via button box, keyboard, mouse, speech, eye movement, and grip force has also been established. We are also equipped with an electronic shop and a small machine shop, providing the capability to fabricate custom MRI coils, animal holders, and special purpose stimulation devices. Other equipment in the scanner rooms includes an Ohmeda Biox 3700 Pulse oximeter, a Sage 351 infusion/withdrawal syringe pump, and a Dinamap 1846 SX Critikon vital signs monitor.

Shared Research/Clinical Skyra 3T MRI Scanner (BHI)

The shared MRI unit is a Siemens Medical Solutions (Malvern, PA) 3.0 Tesla Skyra MRI scanner, a full body scanner (70 cm bore) with Sonata gradient set (gradient amplitude of 40mT/m, maximum slew rate of 200T/m/sec).  The system is actively shielded and is equipped with 32 RF receiver channels and the total imaging matrix (TIM) suite.  Multiple coils are available for the systems, including a, 20 channel head matrix coil, two body matrix 8 channel flex coils, 8 channel head coil, 4 channel carotid coil and a 24 channel spine coil.

This scanner runs Siemens Syngo VE11A software and has a number of advanced Siemens product sequences including parallel imaging, SWI, BLADE, Diffusion Tensor Imaging (DTI) & Tractography. Auto Align feature for reproducible slice positioning based on a 3D MR brain atlas, BOLD imaging and in-line analysis suite with 3D PACE realtime motion correction, advanced cardiac package, and single and multi-voxel spectroscopy. A number advanced research sequences including Vessel Size Imaging, quantitative Arterial Spin Labeling, Diffusion Spectrum Imaging (for High Angular Resolution Diffusion Imaging) and Simultaneous Multi-Slice EPI (allowing for sub-second high-resolution whole-brain fMRI data acquisition), 4D phase contrast MR for measuring flow velocity, displacement encoding (DENSE), multi-echo and ultra-short echo time sequences are also available.

Human Positron Emission Tomography (PET) High Resolution Scanner

The PET HRRT scanner is the highest resolution human brain PET scanner available. It consists of concentric rings of LSO and LYSO detectors to provide depth of interaction information.  Because of this, the resolution is 2mm and fairly isotropic throughout the field of view.  Data is collected in list mode and reconstructed in 3D on a 16-node dual processor computer cluster.  Attenuation scanning is performed very rapidly in singles mode with a 30 mCi 137Cs point source.  This scanner provides state-of-the-art PET imaging for human or animal neuro studies or whole body imaging for animals or other objects less than 20 cm across.

The HRRT scanner room is a 400 sq. ft. room with 20 feet of bench space and a sink. The room is equipped with anesthesia gases and exhaust and a pneumatic tube system for delivery of doses from the cyclotron suite.  The pneumatic tube system terminates in a lead cave that contains a Capintec CRC-712M dose calibrator.  Stainless steel tubes from the cyclotron have been installed to deliver radiolabeled gases directly to the room from the cyclotron. The room also contains two 4 cu. ft. lead caves for storage of phantoms and calibration sources.

The PET/HRRT scanner control room (110 sq. ft.) contains two computer workstations, hardcopy output devices, the computers for controlling the scanner, and the video monitor command center, and a wide range of peripherals to read and write tapes and optical disks.

Peripheral quantitative computed tomography (pQCT)

The XCT 2000 pQCT Bone Densitometer is a type of low-dose prescription x-ray device used to perform non-invasive measurements of bone mineral density (BMD) in a peripheral part of the body, such as the forearms or legs. The pQCT technique allows the calculation of bone strength with respect to bending, torsion, and compression from bone's cross sectional geometry. Additional morphometric parameter like endosteal and periosteal perimeter and bone cross sectional area are accessible in vivo. pQCT measurements at tibia or radius are widely performed in clinical routine.

Animal Imaging

9.4T Bruker Animal MRI System. A 9.4T/21-cm Bruker animal MR imaging/spectroscopy system is housed in the Whitehead Biomedical Research Building in approximately 400 square feet of space. The magnet is actively shielded to reduce the extent of the fringe field. The imaging console is interfaced with a Bruker AVANCE spectrometer driven by a LINUX workstation and Bruker ParaVision 5.1 imaging software. The system is equipped with actively decoupled RF coils (volume coil as a transmitter and the surface coil as a receiver) with 2-RF channels: one with 1000 Watt RF amplifier for 1H NMR studies and the other with 800 Watt broadband amplifier (frequency range from 6 to 365 MHz) for X-nucleus NMR studies. A quadrature volume coil optimized for imaging rat brains and a variety of surface coils are also available. The scanner is equipped with a state-of-the-art BFG 200/115-S-14 12-cm diameter gradient insert from RRI (maximum gradient strength 675 mT/m, 120 µs rise time), two actively shielded Bruker BGA gradient sets, BGA-12 (12 cm, maximum gradient strength of 400 mT/m, 88 µs rise time) and BG-6 gradient set (6 cm, maximum gradient strength of 1000 mT/m, 55 µs rise time), all driven by Copley 200A/300V Gradient Amplifiers. Peripheral equipment including a) physiological signals monitoring system (BioTrig), used for synchronizing MR acquisitions with ECG or respiration triggering signals; b) animal anesthesia and physiology maintenance system; c) a comprehensive set of RF coils, suitable for studying different sized animals, different tissues and locations, and different nuclei including proton, 17O, 13C, 19F, an 31P; d) acoustic, optic, and electrical stimulation accessories for functional study. This system is suitable for studying mice, rats, ferrets and other small animals.

MicroPET/CT animal Scanner. The Inveon microPET is a lutetium oxyorthosilicate (LSO)–based preclinical PET scanner used primarily for small rodent imaging. The system is comprised of 64 detector blocks arranged in 4 contiguous rings, with a crystal ring diameter of 16.1 cm and an axial extent of 12.7 cm. The energy resolution is 14.6 %, sensitivity of 6.7%, scatter fraction of 8-17 % and spatial resolution of 1.8 mm FWHM. Data acquisition options include static, dynamic, respiratory gating and cardiac gating.  This represents the best available PET imaging for small objects.  The microPET scanner can be docked to the microCT scanner to form a microPET/microCT system.

The Inveon microCT Module is a high resolution 3D anatomic computed tomography (CT) imaging system for laboratory animal studies.  The x-ray source is for high speed whole mouse or rat preclinical x-ray CT studies and other applications requiring resolution down to 30 microns. The system is capable of respiratory and cardiac gating.  The scanner can be docked to the microPET scanner to form a microPET/microCT system.  This ultra-high speed implementation of a modified Feldkamp cone beam reconstruction algorithm exploits recent developments in microprocessor technology to provide reconstructed image volumes within seconds of scan completion.  The base reconstruction system uses two Xeon processors to generate 512 x 512 x 768 voxel image volumes in real time during a scan.  Larger volumes are quickly reconstructed in multiple passes.

MAJOR EQUIPMENT

Updated 1 July 2022

Major Equipment for the Center for Systems Imaging Core (CSIC) Users

CENTER FOR SYSTEMS IMAGING CORE (CSIC)

Magnetic Resonance Imaging (MRI)

The Center for Systems Imaging Core (CSIC) operates three full-time research dedicated Siemens Magnetom Prisma 3T MR scanners, and a shared clinical/research 3T wide-bore Siemens Skyra scanner. With multiple human research 3T MRI scanners, MRI studies can be effectively distributed across the Emory community. Studies that require close proximity to Emory University Hospital (EUH) or studies performed on in-patients can be performed on the scanner located on the ground floor of the hospital (CSI-EUH). Outpatient studies, where convenience of parking and more flexible scheduling is required can be performed at scanner located at the Wesley Woods (WW) campus (CSI-WW). Both scanners have been recently upgraded to the PrismaFIT platform and VE11C software. Studies which require a wide-bore scanner or have a study population located at the Brain Health Institute (BHI) at Executive Park can use the Prisma scanner located there or the Skyra scanner next door for up to two hours per day (CSI-BHI).

Research Dedicated 3T Prisma MRI Scanners (EUH and WW)

MRI Scanners. Magnetom Prisma whole-body MR systems are equipped with a state-of-the art gradient system with a maximum (per axis) strength of 80 mT/m and slew rate of 200 T/m/sec, 64 independent RF receiver channels capable of 204 receiver connections, and a 2-channel RF transmitter. Multiple coils are available, including a 64-channel head/neck coil with 52 channels for imaging of the head region, a 32-channel head-only coil, a 20-channel head/neck coil, spine array coil, flexible chest coil, large and small flexible coil for extremity imaging, Tx/Rx CP Head Coil for large no-cap head space, and a ³¹P dual-tune flexible coil (only for Prisma@EUH) for phosphor spectroscopy. All scanners are running the VE11C version of the Siemens Syngo software. In addition, the scanners are equipped with DirectRF and DirectConnect technology, providing a significant increase in signal-to-noise ratio. The Prisma scanner platform allows efficient acquisition of high-resolution fMRI and DTI images with protocols compatible to those released by the Human Connectome Project. Furthermore, the Prisma scanner located at EUH is equipped with multinuclei spectroscopy and additional shimming power for improved magnetic resonance spectroscopy. A number of advanced research sequences are also available, including Vessel Size Imaging, quantitative Arterial Spin Labeling, Diffusion Spectrum Imaging (for High Angular Resolution Diffusion Imaging) and Simultaneous Multi-Slice EPI (allowing for sub-second high-resolution whole-brain fMRI data acquisition), 4D phase contrast MR for measuring time-resolved flow velocity, displacement encoding with stimulate echoes (DENSE), and multi-echo and ultra-short echo time sequences. With our master research agreement with the vendor, advanced work-in-progress MR sequences from the vendor, collaborators from other institutions, or developed sequences locally can be deployed.

Stimulus and response system for functional MRI. All scanners are equipped with peripheral systems for fMRI. Stimulus/response controls for behavioral tasks concurrent with fMRI are supported by an array of hardware specifically designed to allow investigator flexibility and precision. Visual presentation at EUH and WWHC sites are provided by a high resolution LCD projection system (1400x1050 SXGA, 4200 lumens, 1300:1 ratio) delivered from the back of the suite onto a custom fit screen mounted within the bore behind the participant’s head. The EP12 sites are equipped with Cambridge Research Systems BOLDScreen MRI compatible LED displays. Audio presentation is provided by an Avotec Silent Scan 3100 that has been calibrated to maintain sound pressure levels that are dependent directly on input (flat frequency response +/- 4dB, 200-4500Hz range). A fiber-optic ergonomic bilateral button response system from Psychology Software Tools exists, as well as a control unit to support custom response shapes (joysticks, steering wheels, wands) from Current Designs. Hardware are connected through a single switch that signals TTL trigger pulses and allows connectivity to an investigator’s laptop with non-proprietary connections (USB, 1/8” minijack audio, VGA & DVI). A dedicated stimulus and response monitoring computer running Eprime 2.0 and Presentation stimulus programming software also exists. An OptoAcoustics FOMRI MRI-compatible microphone featuring advanced active noise cancellation technology is available for speech fMRI paradigms. CSI-EUH MR scanner is also equipped with multi-nuclei option. Currently a 31P/1H dual tune flexible coil is equipped and is applicable to phosphor MRS and metabolism studies.

CSI-WW: Other Equipment. A Biopac MP150 (Goleta, CA) MRI-compatible physiological response measurement system is available for collecting peripheral physiological measures. The MP150 system provides high resolution (16 bit), variable sample rates for analog and calculation channels, 16 analog inputs and two analog outputs, digital I/O lines (automatically control other TTL level equipment), and 16 online calculation channels. The MP150 System provides high-speed acquisition (400 kHz aggregate) via an Ethernet connection to a host computer. AcqKnowledge, the Biopac control and analysis software package is used to control the acquisition and can be used for data analysis. Available physiological measures are cardiac pulse, heart rate, heart period, respiratory sinus arrhythmia, respiration and electrodermal activity. The physiological measurements recorded by Biopac can be viewed real-time on a dedicated laptop computer through the Biopac data acquisition software. All responses can be recorded in MatlabTM, text or proprietary Biopac software formats, for retrospective analysis. A MEDRAD (Warrendale, PA) Power Injector system for contrast administration is also available.

CSI-WW: Mock MRI Scanner. A mock MR scanner is set up in the Wesley woods facility. This mock scanner is similar in appearance to the Siemens MRI scanners. It provides stimulus presentation and scanner noise emulations and is used to familiarize pediatric subjects with MRI scanner operation and to acclimate them to the MR scanning environment.

CSI-EUH: Other Equipment. Peripheral equipment, including computers and software for paradigm generation, setup for stimulus presentation, devices for recording behavioral data and physiological parameters including heartbeat, respiration, blood pressure, eye movement, ECG, EEG, and EMG are also established for operation concurrent with MR acquisition. Stimulus generation and presentation setup allows us to present acoustic, electric, and vibrational stimuli and oral and venous administration of liquids. Setup for response via button box, keyboard, mouse, speech, eye movement, and grip force has also been established. We are also equipped with an electronic shop and a small machine shop, providing the capability to fabricate custom MRI coils, animal holders, and special purpose stimulation devices. Other equipment in the scanner rooms includes an Ohmeda Biox 3700 Pulse oximeter, a Sage 351 infusion/withdrawal syringe pump, and a Dinamap 1846 SX Critikon vital signs monitor.

Shared Research/Clinical Skyra 3T MRI Scanner (BHI)

The shared MRI unit is a Siemens Medical Solutions (Malvern, PA) 3.0 Tesla Skyra MRI scanner, a full body scanner (70 cm bore) with Sonata gradient set (gradient amplitude of 40mT/m, maximum slew rate of 200T/m/sec). The system is actively shielded and is equipped with 32 RF receiver channels and the total imaging matrix (TIM) suite. Multiple coils are available for the systems, including a, 20 channel head matrix coil, two body matrix 8 channel flex coils, 8 channel head coil, 4 channel carotid coil and a 24 channel spine coil.

This scanner runs Siemens Syngo VE11A software and has a number of advanced Siemens product sequences including parallel imaging, SWI, BLADE, Diffusion Tensor Imaging (DTI) & Tractography. Auto Align feature for reproducible slice positioning based on a 3D MR brain atlas, BOLD imaging and in-line analysis suite with 3D PACE realtime motion correction, advanced cardiac package, and single and multi-voxel spectroscopy. A number advanced research sequences including Vessel Size Imaging, quantitative Arterial Spin Labeling, Diffusion Spectrum Imaging (for High Angular Resolution Diffusion Imaging) and Simultaneous Multi-Slice EPI (allowing for sub-second high-resolution whole-brain fMRI data acquisition), 4D phase contrast MR for measuring flow velocity, displacement encoding (DENSE), multi-echo and ultra-short echo time sequences are also available.

Computing Facilities

The CSIC is equipped with a state-of-the art computing facility consisting of a twenty-four nodes linux mini cluster, disk RAIDs with 529 TiB total storage capacity, a full rack capable of supporting up to 16U calculation nodes, including three NVidia Tesla GPU enhanced nodes, and an automated off-site back-up server with 394TiB backup storage configure to bi-weekly rotation and one-year time machine backup scheme. For data processing and analysis, Matlab, IDL, LCmodel, SPSS, SPM, fsl, AFNI, freesurfer, ANTs, MrTrix, Slicer, tensorflow, and a variety of python based pipelines are installed and available on our cluster. VMware and Oracle VirtualBox are also available for special virtualization need. The computer cluster is also a dicom receiving server open to all collaborating PIs for data storage and analysis purpose.

9.4T Bruker Animal MRI System

A 9.4T/21-cm Bruker animal MR imaging/spectroscopy system is housed in the Whitehead Biomedical Research Building in approximately 400 square feet of space. The magnet is actively shielded to reduce the extent of the fringe field. The imaging console is interfaced with a Bruker AVANCE spectrometer driven by a LINUX workstation and Bruker ParaVision 5.1 imaging software. The system is equipped with actively decoupled RF coils (volume coil as a transmitter and the surface coil as a receiver) with 2-RF channels: one with 1000 Watt RF amplifier for 1H NMR studies and the other with 800 Watt broadband amplifier (frequency range from 6 to 365 MHz) for X-nucleus NMR studies. A quadrature volume coil optimized for imaging rat brains and a variety of surface coils are also available. The scanner is equipped with a state-of-the-art BFG 200/115-S-14 12-cm diameter gradient insert from RRI (maximum gradient strength 675 mT/m, 120 usec risetime), two actively shielded Bruker BGA gradient sets, BGA-12 (12 cm, maximum gradient strength of 400 mT/m, 88 usec risetime) and BG-6 gradient set (6 cm, maximum gradient strength of 1000 mT/m, 55 usec risetime), all driven by Copley 200A/300V Gradient Amplifiers. Peripheral equipment including a) physiological signals monitoring system (BioTrig), used for synchronizing MR acquisitions with ECG or respiration triggering signals; b) animal anesthesia and physiology maintenance system; c) a comprehensive set of RF coils, suitable for studying different sized animals, different tissues and locations, and different nuclei including proton, 17O, 13C, 19F, an 31P; d) acoustic, optic, and electrical stimulation accessories for functional study. This system is suitable for studying mice, rats, ferrets and other small animals.

Cyclotron and Radiochemistry

CSIC’s radiochemistry lab is directed by Dr. Mark Goodman, PhD and Ron Crowe (a licensed Radiopharmacist).  The lab houses a Siemens RDS 111 multiport, self-shielded, automated cyclotron producing a 11 MeV, 50 µA proton beam. The cyclotron is equipped with targets for the routine production of curie amounts of [¹⁸F]fluoride, [¹¹C]carbon dioxide, and [¹⁵O]oxygen and millicurie amounts of [¹³N]ammonia. The radiochemistry area is a 2,100 square foot cyclotron vault and laboratory which includes four master slave manipulator arm-equipped hot cells, five mini-cells, one Siemens computer programmable two reaction vessel radiochemical processing unit, one GE TracerLab FXN unit, one GE Fastlab unit, one Siemens automated oxygen-15 water synthesis module, two GE PETtrace carbon-11 methyl iodide modules, one clean room , hot and cold waste systems and ventilation chemical and radiation monitoring systems. A pharmaceutical grade germanium-68/gallium-68 generator is located in the clean room for routine production of as [⁶⁸Ga]GaCl for the preparation of as [⁶⁸Ga]-radiopharmaceuticals for preclinical small animal and human clinical and research imaging studies. The radiochemistry laboratory is equipped with four pneumatic tube systems located in the four hot cells for rapid delivery of radiopharmaceuticals. The radiochemistry laboratory is fully equipped with a variety of modern analytical instruments which include one Carroll and Ramsey Associates eleven probe radiation detection system, one Waters Alliance radio-HPLC unit that is configured with UV/Vis and IN/US Radiometric detectors and one Waters Breeze radio-HPLC units that are configured with  UV/Vis, and Bioscan Radiometric detectors, one Lab Logic Scan-RAM radioactivity thin-layer chromatography system, two electrically activated rheodyne HPLC injectors, eight manual rheodyne HPLC injectors and 4 Waters' 515 HPLC pumps, one Bioscan hot cell radiometric detector, one Agilent 6890N radio-gas chromatograph equipped with a thermal conductivity and flame ionization  detectors, one Lab Logic Gamma-RAM Radio-GC detector, one Ortec sodium iodide detector and well counter/multichannel analyzer, two Capintec 712M dose calibrators with four remote ionization chambers and four remote readouts and four Mettler electronic balances. The radiopharmacy routinely prepares [⁶⁸Ga]Netspot, [¹⁸F]FACBC aka Axumin, [¹⁵O]water, [¹¹C]PIB and [¹⁸F]T807 for human imaging studies.

Positron Emission Tomography (PET) High Resolution Scanner

The PET HRRT scanner is the highest resolution human brain PET scanner available. It consists of concentric rings of LSO and LYSO detectors to provide depth of interaction information. Because of this, the resolution is 2mm and fairly isotropic throughout the field of view. Data is collected in list mode and reconstructed in 3D on a 16-node dual processor computer cluster. Attenuation scanning is performed very rapidly in singles mode with a 30 mCi 137Cs point source. This scanner provides state-of-the-art PET imaging for human or animal neuro studies or whole body imaging for animals or other objects less than 20 cm across.

The HRRT scanner room is a 400 sq. ft. room with 20 feet of bench space and a sink. The room is equipped with anesthesia gases and exhaust and a pneumatic tube system for delivery of doses from the cyclotron suite. The pneumatic tube system terminates in a lead cave that contains a Capintec CRC-712M dose calibrator. Stainless steel tubes from the cyclotron have been installed to deliver radiolabeled gases directly to the room from the cyclotron. The room also contains two 4 cu. ft. lead caves for storage of phantoms and calibration sources.

The PET/HRRT scanner control room (110 sq. ft.) contains two computer workstations, hardcopy output devices, the computers for controlling the scanner, and the video monitor command center, and a wide range of peripherals to read and write tapes and optical disks.

MicroPET/CT Animal Scanner

The Inveon microPET is a lutetium oxyorthosilicate (LSO)–based preclinical PET scanner used primarily for small rodent imaging. The system is comprised of 64 detector blocks arranged in 4 contiguous rings, with a crystal ring diameter of 16.1 cm and an axial extent of 12.7 cm. The energy resolution is 14.6 %, sensitivity of 6.7%, scatter fraction of 8-17 % and spatial resolution of 1.8 mm FWHM. Data acquisition options include static, dynamic, respiratory gating and cardiac gating. This represents the best available PET imaging for small objects. The microPET scanner can be docked to the microCT scanner to form a microPET/microCT system.

The Inveon microCT Module is a high resolution 3D anatomic computed tomography (CT) imaging system for laboratory animal studies. The x-ray source is for high speed whole mouse or rat preclinical x-ray CT studies and other applications requiring resolution down to 30 microns. The system is capable of respiratory and cardiac gating. The scanner can be docked to the microPET scanner to form a microPET/microCT system.This ultra-high speed implementation of a modified Feldkamp cone beam reconstruction algorithm exploits recent developments in microprocessor technology to provide reconstructed image volumes within seconds of scan completion. The base reconstruction system uses two Xeon processors to generate 512 x 512 x 768 voxel image volumes in real time during a scan. Larger volumes are quickly reconstructed in multiple passes.

Peripheral quantitative computed tomography (pQCT)

The XCT 2000 pQCT Bone Densitometer is a type of low-dose prescription x-ray device used to perform non-invasive measurements of bone mineral density (BMD) in a peripheral part of the body, such as the forearms or legs. The pQCT technique allows the calculation of bone strength with respect to bending, torsion, and compression from bone's cross sectional geometry. Additional morphometric parameter like endosteal and periosteal perimeter and bone cross sectional area are accessible in vivo. pQCT measurements at tibia or radius are widely performed in clinical routine.

FACILITIES & OTHER RESOURCES

Updated 1 September 2020

Fields Relevant for the Biostatistics Collaboration Core (BCC)

The Biostatistics Collaboration Core (BCC) offers comprehensive bioinformatics, statistical, and computational collaboration to the University community. The primary mission of BCC is collaborating with investigators to choose appropriate study design for quantitative analysis and to assure appropriate implementation of statistical methodology in research. The BCC offers a complete range of services including study design; database design and management; bioinformatics needs; statistical analysis for abstracts and grants; and supporting the presentation and publication of research results. The faculty, staff, students, and facilities of the BCC are a part of the Department of Biostatistics and Bioinformatics at Rollins School of Public Health.

The Biostatistics Collaboration Core (BCC) is a part of the Department of Biostatistics and Bioinformatics at the Rollins School of Public Health. The department occupies the entire third floor and more than half of the second floor of the Grace Crum Rollins building located at 1518 Clifton Rd. Faculty, staff and doctoral student offices, a computer laboratory, and a library/conference room, make up the 6,788 square feet of usable space. The Department of Biostatistics and Bioinformatics currently has 29 doctoral level faculty, 5 jointly appointed faculty members, 7 associate faculty members, 1 emerita faculty, and 18 adjunct faculty. The department has roughly 100 masters and doctoral students presently enrolled as degree seeking students.                                                                       

FACILITIES & OTHER RESOURCES

Updated 1 July 2022

Fields Relevant for the Emory Glycomics and Molecular Interactions Core (EGMIC)

EMORY GLYCOMICS AND MOLECULAR INTERACTIONS CORE (EGMIC)

The Emory Glycomics and Molecular Interactions Core (EGMIC), one of the Emory Integrated Core Facilities (EICF), is located in a laboratory in Room 175 in the Whitehead Biomedical Research Building. The dedicated laboratory space for ECGC totals approximately 1,500 sq. ft. and includes state-of-the-art equipment for printing and interrogating glycan microarrays for determining the binding specificity of glycan binding proteins and organisms. An additional 500 sq. ft. laboratory in Room 4110 in the O. Wayne Rollins Research Center houses instrumentation that quantifies molecular interactions using label-free methods including surface plasmon resonance with a BiaCoreX100 and isothermal titration calorimetry using a MicroCal Auto-iTC200. In the same room, we also host a Bruker UltraFlexII MALDI-TOF/TOF for glycomics and proteomic analyses, as well as general molecular weight characterization for other biomolecules including nucleic acids and intact proteins.

The EGMIC provides four major types of service

·       Functional glycomics including glycan microarray screening (Consortium for Functional Glycomics array of > 500 defined glycans, sialylated oligosaccharides array, human blood group glycan array, and others), chemical release of glycans from glycoconjugates, production of Tagged Glycan Library, production and analysis of Shotgun Glycan Microarray.

·       Glycomics analysis: glycomic profiling of molecular masses of glycans in mixtures released from purified glycoprotein, mucins, glycolipids, as well as cultured cells, tissues, or organs which can generate compositional information on glycans and can provide predictions of structures. 

·       Custom Microarray Printing of glycans, protein and providing microarray analysis

·       Convenient access to Biacore™ and MicroCal™ instruments for the study of molecular interactions including protein-glycan, protein-protein, protein-small molecules.

MAJOR EQUIPMENT

Updated 1 July 2022

Major Equipment for Emory Glycomics and Molecular Interactions Core (EGMIC) Users

EMORY GLYCOMICS AND MOLECULAR INTERACTIONS CORE (EGMIC)

Quanterix (Aushon) 2470 Arrayer – Microarray Printing Platform: Aushon’s 2470 microarrayer produces high quality arrays of DNA, proteins, glycans, polysaccharides, cell lysates and a variety of other samples using its proprietary soft touch deposition technology. The 2470 is a highly engineered platform designed with quality, reliability, flexibility and true walk-away automation in mind. Our unique deposition technology enables printing of even complex biological samples onto a broad range of substrates such as slides, membranes, microtiter plate wells, disks, wafers and chips.

The 2470 Arrayer has unmatched versatility, able to print any sample type onto substrates with unique shapes and chemistries as well as the most delicate of substrates such as nitrocellulose and silicon chips. From genomic materials to antibodies and cellular lysates, Aushon’s unique solid pin architecture reliably produces arrays of exceptional quality.

InnoScan® 1100 AL: The InnoScan 1100 AL is a high-resolution 3-color fluorescence scanner. With a resolution of up to 0.5µm/pixel, this scanner can scan a whole slide into high quality image. Combining high performance with full automation, InnoScan 1100 AL is ideal for high-density or three-color microarrays as well as for cell microarrays. Characterized by its ease of use, performance and versatility, the InnoScan 1100 AL is the ideal tool for cell microarrays as well as three-color microarrays.

·       High quality images: With a resolution of up to 0.5µm/pixel or a 20x objective equivalent, the InnoScan 1100 AL is the highest resolution microarray scanner on the market. This combined with a real time autofocus system and confocal PMT detection; the InnoScan 1100 AL provides high-quality images for detailed analysis of your microarrays.

·       Easy automation: Provided with a user-friendly image acquisition software and 24-slide autoloader, the InnoScan 1100 AL is capable of fully automated scanning of 24 slides at a time.

·       Multiplexed whole slide imaging: The InnoScan 1100 AL is capable of scanning any microscope slide with various substrates: cells, tissue, proteins, DNA, glycans, peptides and others. Equipped with three excitation channels, it empowers users with more multiplexing capabilities, thus allowing the analysis of several samples or markers on the same slide.

BiaCore™ X100: The Biacore X100 is a complete solution for biochemistry, molecular biology, or other research laboratories involved in the study of molecular interactions. The system contains all the key functionalities needed for day-to-day molecular interaction research with the purpose of understanding protein function and biological mechanisms.

·       Real-time insights into protein function & biological mechanisms

·       Kinetics, affinity, specificity and concentration analysis in one system

·       Define structure/function relationships

·       Understand the dynamics of molecular pathways

·       In development and research studies, select promising molecules that could be novel targets for research use, diagnostics, or therapy.

·       Develop and run assays for interactions involving LMW compounds

Biacore systems are used in areas such as pharmaceutical drug discovery, antibody characterization, proteomics, immunogenicity, biotherapeutic development and manufacture, and many life science research applications. A range of systems meet specific application needs. Customers include leading research centers, all of the leading global pharmaceutical companies, and many biotechnology companies.

MicroCal Auto-iTC200: The MicroCal ITC isothermal titration calorimeters all allow direct, label-free in solution measurement of binding affinity and thermodynamics in a single experiment, enabling the accurate determination of binding constants (KD), reaction stoichiometry (n), enthalpy (ΔH) and entropy (ΔS). This provides a complete thermodynamic profile of the molecular interaction. ITC goes beyond binding affinities and can elucidate the mechanisms underlying molecular interactions.

The MicroCal Auto-iTC200 is a fully automated, low volume, highly sensitive isothermal titration calorimeter. It delivers direct, label-free in solution measurement of all binding parameters in a single experiment. Applications include characterizing molecular interactions of small molecules, proteins, antibodies, nucleic acids, lipids and other biomolecules. It can also be used to measure enzyme kinetics.

Bruker UltraFlexII MALDI-TOF/TOF: Features high sensitivity, resolution and mass accuracy of MALDI-TOF and TOF/TOF technology for high-success expression proteomics and advanced biomarker discovery studies. It is also routinely used for glycomics profiling. MALDI-MS is easy to operate and is especially convenient for characterization of large biomolecules such as proteins, nucleic acids and polymers due to its high mass limit.

FACILITIES & OTHER RESOURCES

Updated: 1 July 2022

Specific Fields Relevant for Emory Flow Cytometry Core (EFCC) Users

EMORY FLOW CYTOMETRY CORE (EFCC)

The Emory Flow Cytometry Core (EFCC), one of the Emory Integrated Core Facilities (EICF), provides unique services to Emory clinical and basic researchers. The central mission of the EFCC is to provide a top-tier flow cytometry resource that are widely available to the Emory research community and that integrates cutting-edge cytometric technologies with downstream analyses. The EFCC’s primary focus is to provide high-quality sorting services to its clientele, whether it is bulk sorting of multiple populations of various phenotypes or single- or multiple-cell deposition into culture plates of various size.

The EFCC offers advanced polychromatic flow cytometry training on its analyzer cytometer and consultation services for experimental design. The EFCC is located in the Dental Building at 1462 Clifton Rd., N.E. and Rollins Research Bldg at 1518 Clifton Rd., N.E. and has roughly 1500 sq. ft. of space divided into three laboratories.

MAJOR EQUIPMENT

Updated: 1 July 2022

Specific Fields Relevant for Emory Flow Cytometry Core (EFCC) Users

EMORY FLOW CYTOMETRY CORE (EFCC)

The Emory Flow Cytometry Core (EFCC), one of the Emory Integrated Core Facilities (EICF), contains two BD FACSAria II 5-laser, 17-color sorters each capable of sorting 4 populations at once. In addition, both sorters can accommodate single- or multiple-cell deposition into culture plates. EFCC also houses two high-spec analyzer cytometers: 5 laser, 18-color BD LSR II and a 5-laser, 24-color BD Symphony A3.

FACILITIES AND RESOURCES

Updated 22 June 2022

Fields Relevant for the Emory Gnotobiotic Animal Core (EGAC)

EMORY MICROBIOME CORE FACILITIES

The Emory Integrated Core Facilities (EICF) support microbiome studies by synergizing the skills and resources of three core facilities, namely The Emory Gnotobiotic Animal Core (EGAC), The Emory Integrated Genomics Core (EIGC), and The Emory Integrated Computational Core (EICC). Workflows have been optimized between the three cores to form a pipeline whereby gnotobiotic studies are undertaken within the EGAC, sequencing of microbiome 16S rDNA from gnotobiotic studies undertaken by the EIGC, followed by expert analysis of the generated sequence data and characterization of the microbial alpha and beta diversities undertaken by the EICC.

EMORY GNOTOBIOTIC ANIMAL CORE (EGAC)

Introduction: The Emory Gnotobiotic Animal Core (EGAC), one of the Emory Integrated Core Facilities (EICF), is located in the five-story, 200,000-square-foot Health Sciences Research Building (HSRB), situated in rooms next to the Specific Pathogen Free (MPF) murine housing, as well as the Transgenic Mouse and Gene Targeting Core. The facility contains sixteen 3’ foot wide rigid isolators (Parkbio), each with the capacity to house 12 mice cages each. Each cage has a maximum capacity of 5 mice per cage. Class II biological cabinets are available to investigators for experimental use.

Animal welfare: The facility has a dedicated technician to monitor murine health. The facility is run under Emory University’s IACUC approved Standard Operating Procedures which oversees and certifies that care and use of the animals is ethical and humane. The IACUC oversight is implemented by an ongoing review and approval of the facility by way of written animal use protocols submitted for review by IACUC committee members. In addition, a semiannual inspection of all areas where animals are housed or undergo procedures is undertaken within the facility. Federal regulations, veterinary standards of care, campus policies, and facility standard operating procedures are used by the IACUCs in their evaluations of animal use.

Microbiological Testing: We employ rigorous microbiological testing of all autoclaved material entering the isolators, including the food, water and bedding. We also regularly monitor germ-free mice within isolators

and periodic control necropsies. Our tests include 1) real time quantitative PCR amplification of the V4 region 16S rRNA gene, 2) plating of fecal samples on BBL Brain Heart infusion with 10% Sheep Blood plates (nonselective controls for all strains) and incubation at 37ºC for 7 days, 3) Incubation in Thioglycollate medium with indicator, a medium used for the isolation and cultivation of aerobes, anaerobes and microaerophiles that are not excessively fastidious, and 4) Gram stain, which is a general visual examination for the presence of bacteria, and distinguishes between Gram-positive and Gram-negative organisms.

Gnotobiotic colonization: For colonization studies, 5-week-old germ-free mice are be inoculated with a either 1) a single microbe (mono-colonization) with a single bacterium), or 2) a defined finite group of microbes such as altered Schaedler flora (ASF) is a community of eight bacterial species: two Lactobacilli, one Bacteroides, one spiral bacteria of the Flexistipes genus, and four extremely oxygen sensitive (EOS) Fusobacterium species. The bacteria are selected for their dominance and persistence in the normal microflora of mice, and for their ability to be isolated and grown in laboratory settings. Germ-free animals, mainly mice, are infected with ASF for the purpose of studying the gastrointestinal (GI) tract. The standardized microbial cocktail enabled the controlled study of microbe and host interactions, role of microbes, pathogen effects, and intestinal immunity and disease association. Also, compared to germfree animals, ASF mice have fully developed immune system, resistance to opportunistic pathogens, and normal GI function and health, and are a great representation of normal mice, or 3) a polymicrobial population sourced from another mouse or a human clinical sample, for example a humans or animals that has been treated with an antibiotic which may be used to establish whether it is the altered microflora diversity that triggers changes in organismal physiology. Microbes may be introduced directly into the stomach with a 24-gauge ball-tipped gavage needle, or because mice are coprophagic, polymicrobial microbiome transfer from mouse to mouse may be done by introducing fecal pellets into the recipient cage. Routine microbiological testing to establish that the desired microbiome diversity is maintained throughout the experiment is done collecting stool samples, purification of DNA from the samples, and PCR amplification of the V4 region of the 16S rRNA gene from the sample. The PCR product are then sequenced and output files processed using the QIIME and MOTHUR pipelines. In addition, to gnotobiotic isolation within isolators, the facility will be equipped with the Tecniplast ISOcage system allowing gnotobiotic isolation at 36 single cage level, enabling multiple studies on the same rack.

ISOcage Tecniplast Bioexclusion System: Precise modulation of the microbiome is increasingly been appreciated as feasible approach to positively impact health and disease. However, heterogeneity of the microbiome between murine colonies housed in various facilities nationwide represent a tangible challenge to scientific rigor and reproducibility. Indeed, incongruent results have been observed between facilities when mice of the same phenotype were subjected to the same assays. We have developed a facility to directly control for microbiome heterogeneity by, where feasible, undertaking our assays in mice gnotobiotically colonized them with a defined flora. We undertake this by housing our mice in within our cutting edge Tecniplast ISOcageP Bioexclusion system. These are airtight individual mouse cages with high positive pressure that are specifically designed for germ-free, gnotobiotic and bioexclusion studies. The ISO cage system is the latest design for gontobiotics and germ-free animals because it allows researchers to undertake up to 36 simultaneous gnotobiotic studies, compared to only one study at a time in conventional multi-cage gnotobiotic isolators. For gnotobiotic experiments, mice can be initially raised under germ-free conditions. After weaning (3 weeks) mice will be transferred to an ISOcage cage.

For experiments with a fully characterized controlled microbiome background, mice may be gnotobiotically colonized with Altered Schaedler Flora (ASF). ASF is a standardized microbial blend of eight bacteria, which allows for the exquisitely meticulous studies in a fully defined microbiome background. Importantly, compared to germ-free animals, ASF-associated mice have normally developed immune system, they have resistance to opportunistic pathogens, and normal gastrointestinal health. They are thus an excellent representative model of normal mice with a defined microbiome. ASF colonization is done by the initial purchase of fecal pellets containing ASF from Taconic Biosciences Inc., which is a commercial supplier of gnotobiotic animals and materials. For probiotics supplementation experiments, ASF colonized mice are fed twice a week and housed in the Tecniplast ISOcageP Bioexclusion system. By this method we can achieve complete scientific reproducibility by undertaking our experiments with a defined background microbiome.  For experiments in this proposal, we will undertake fecal microbiome transplant experiments by isolating the samples from the luminal content od humans. It is imperative that following transplantation, the mice be maintained in bioexclusion conditions using the Tecniplast ISOcageP Bioexclusion system for the duration of the experiment (up to 8-weeks). This approach will eliminate the possibility of any further microbial components entering the transplanted microbiome.

Murine strains bred and held within the facility: The facility currently has two large breeding colonies to maintain strains of C57BL/6J.

Transferring new strains into the facility: Currently, we accept rederived germ-free mice from approved vendors, such as (but not limited to) Taconic Biosciences and The National Gnotobiotic Animal Resource Center at UNC. Mice must be shipped in approved transporters. Mice are transferred into newly set up isolators, and kept as the only genotype in said isolator for 4 weeks, and monitored weekly for germ-free status.     

Dedicated gnotobiotic barrier access suite: For this proposal, we will undertake bone fracture studies in germ-free and gnotobiotic conditions. GF and gnotobiotic mice used in manipulations will be housed within our cutting edge Tecniplast ISOcageP Bioexclusion system. GF and gnotobiotic mice will be transferred within the hermetically sealed ISO cage to a dedicated axenic Biological Safety Cabinet where fracture procedures will be undertaken.

MAJOR EQUIPMENT

Updated: 22 June 2022

Major Equipment for Emory Gnotobiotic Animal Core (EGAC) Users

EMORY GNOTOBIOTIC ANIMAL CORE (EGAC)

The Emory Gnotobiotic Animal Core (EGAC), one of the Emory Integrated Core Facilities (EICF), provides services that include experiments using germ-free mice and mice with defined microbiota. Major equipment in the EGAC includes:

Gnotobiotic semi-rigid isolators (Parkbio): The EGAC contains sixteen 3’ foot wide rigid isolators (Parkbio), each with the capacity to house 12 mice cages each. Each cage has a maximum capacity of 5 mice per cage. The chamber of the gnotobiotic isolator is constructed of polypropylene on five sides. The front panel or window can be either flexible PVC. The chamber of the isolator is 3’ foot wide rigid each with the capacity to house 12 mice cages each. The isolators are versatile and can be used for containment, germ-free and exclusion applications. The isolators have high quality cartridge type HEPA filters on both intake and exhaust air systems that provide top axenic security. The glove sleeve design is very spacious especially in the shoulder area allowing greater freedom of movement making the semi-rigid isolators highly ergonomic. The isolators are durable and made of impact resistant polypropylene construction which doesn't corrode from sterilants.

Tecniplast ISOcageP Bioexclusion system: These are airtight individual mouse cages with high positive pressure that are specifically designed for germ-free, gnotobiotic and bioexclusion studies. The ISO cage system is the latest design for gontobiotics and germ-free animals because it allows researchers to undertake up to 36 simultaneous gnotobiotic studies, compared to only one study at a time in conventional multi-cage gnotobiotic isolators. Features include strong bioexclusion for animal protection through cage level HEPA filter, combining the protection of an isolator with the ergonomics and density of an IVC cage for maximum animal safety, and saves space and costs with multiple studies on the same rack.

FACILITIES & OTHER RESOURCES

Updated: April 2023

Specific Fields Relevant for Emory Integrated Computational Core (EICC) Users

EMORY INTEGRATED COMPUTATIONAL CORE (EICC)

The Emory Integrated Computational Core (EICC), one of the Emory Integrated Core Facilities (EICF), offers comprehensive computational services and bioinformatics pipelines for the analysis of -omics data. The EICC has 1000 sq ft of dedicated office space on the 7th floor of the Woodruff Memorial Research Building that provides for meeting customers, weekly meetings with the members of the Emory Integrated Genomics Core (EIGC), and for monthly meetings of computational service providers from other cores within the EICF.

The EICC operates a small HPC system for short computational jobs. The cluster serves multiple functions related to core projects, including running NGS analysis pipelines, high-performance and parallel computing for disciplines such as proteomics, metabolomics, and imaging. The cluster is composed of 1 head node, 5 high-memory compute nodes, and one GPU node with 4x Tesla V100 GPUs. The cluster has a 2PB local storage array and offers access to Emory Isilon storage (1PB research-grade storage, 500TB of HIPAA compliant storage). A 10 Gbps ethernet switch provides a high-speed Storage Area Network (SAN) fabric. All storage arrays and compute nodes utilize the SAN for data transfer and are configured to connect via the 10 Gbps high-speed network. The cluster is connected to the Internet2 high-speed network for large data transfers to and from external systems. The cluster runs Scientific Linux 7 64-bit operating system on all nodes and utilizes Slurm for job submission and management. Configuration: One head node: 2 x 3.3 GHz 8-core CPUs, 64 GB RAM. Five compute nodes: 4 x 2.2 GHz 16-core CPUs, 512 GB RAM, 10 Gbps ethernet. One GPU node: 2 x 2.3 GHz 16-core CPUs, 384 GB RAM, 4 x nVidia Tesla V-100 GPU with 32 GB RAM.

Amazon Web Services (AWS) is an on-demand delivery of IT resources in the cloud with pay-as-you-go pricing. The AWS infrastructure is highly durable, available, elastic and scalable.  The Emory AWS environment is an AWS environment that is established according to the Emory business, security and compliance practices. Access to the Emory AWS Console must be authenticated with Emory Single sign-on. The virtual private cloud within the environment is protected by the Emory firewall. Secured connection (SSH or RDP) to an EC2 instance must be made from a workstation already located on the Emory Core network or via a VPN tunnel that is authenticated by 2-factor authentication. All AWS services have been reviewed by the Emory Security Team, and specific guidelines about utilizing these services for HIPAA or identifiable health information will be published. Emory University provides access to the Emory AWS environment to researchers as part of the overall IT support for research. AWS computing and data storage expenses, however, are not covered by the university, and must be budgeted for in grant applications. The EICC works with LITS to provide guidance on AWS usage and optimization.

The EICC also provides comprehensive computational services for investigators with analyses performed by an EICC computational/bioinformatics expert for a set fee per project. The EICC also supports an enterprise HIPAA compliant LabKey server for Emory investigators. Collaborators outside Emory can also access this LabKey server infrastructure when collaborating with Emory investigators.

Standard analysis pipelines using other open-source software packages are implemented for DNA/RNA-seq/ChIP-seq/16S microbiome sequencing projects for human, animal, and microbial genomes. We have implemented the QIIME 2 pipeline for microbiome data analyses. Custom tools or other pipelines (such as mothur) are also available. For the analysis of RNA-seq data, we have implemented the STAR and HTseq-count pipeline. Custom tools and pipelines can be developed for specialized projects such as fusion transcript detection. For targeted sequencing, exome sequencing, and whole genome sequencing, we use a custom PEMapper and PECaller pipeline. For variant annotation, we use the bystro.io software package. We have also implemented and analyze data sets with other mapping and variant identification pipelines (BWA, GATK). Substantial capacity exists for these integrated computing resources to support computational/bioinformatic analyses for EICC users. As part of our comprehensive bioinformatics services, EICC also functions as the Bioinformatics Shared Resource for the Winship Cancer Center. We also facilitate collaborations with existing biostatistics/bioinformatics service centers at Emory. These include the Winship Biostatistics and Bioinformatics Shared Resource headed by Dr. Jeffrey Switchenko and the Biostatistics Consulting Core (BCC) headed by Dr. Azhar Nizam.

MAJOR EQUIPMENT

Updated: 1 June 2022

Major Equipment for Emory Integrated Computational Core (EICC) Users

EMORY INTEGRATED COMPUTATIONAL CORE (EICC)

The Emory Integrated Computational Core (EICC), one of the Emory Integrated Core Facilities (EICF), provides computational and bioinformatics services to Emory investigators and is the “digital hub” for the EICF. The EICC has 1000 sq ft of dedicated office space on the 7th floor of the Woodruff Memorial Research Building which provides for meeting customers, weekly meetings with the members of the Emory Integrated Genomics Core (EIGC), and for monthly meetings of computational service providers from other cores within the EICF. Servers and storage are located on the Emory campus in a climate controlled and secure data center. The EICC infrastructure and services include:

Computational Resources:

EICC Cluster: The EICC offers comprehensive computational services and bioinformatics pipelines for the analysis of -omics data. The EICC operates a small HPC system for short computational jobs. The cluster serves multiple functions related to core projects, including running NGS analysis pipelines, high-performance and parallel computing for disciplines such as proteomics, metabolomics, and imaging, hosting personal data analysis platforms such as Galaxy. The cluster is composed of 1 head node, 5 high-memory compute nodes, and 1 GPU node. The cluster has a 2PB local storage array and offers access to Emory Isilon storage (1PB research-grade storage, 500TB of HIPAA compliant storage). A 10 Gbps ethernet switch provides a high-speed Storage Area Network (SAN) fabric. All storage arrays and compute nodes utilize the SAN for data transfer, and are configured to connect via the 10 Gbps high-speed network. The cluster is connected to the Internet2 high-speed network for large data transfers to and from external systems. The cluster runs Scientific Linux 7 64-bit operating system on all nodes and utilizes Slurm for job submission and management. Configuration: One head node: 2 x 3.3 GHz 8-core CPUs, 64 GB RAM. Five compute nodes: 4 x 2.2 GHz 16-core CPUs, 512 GB RAM, 10 Gbps ethernet. One GPU node: 2 x 2.3 Ghz 16-core CPUs, 384 GB RAM, 4 x nVidia Tesla V-100 GPUs with 32 GB RAM, 10 Gbps ethernet.

Amazon Web Services (AWS) Cloud Computing: Amazon Web Services (AWS) is an on-demand delivery of IT resources in the cloud with pay-as-you-go pricing. The AWS infrastructure is highly durable, available, elastic and scalable.  The Emory AWS environment is an AWS environment that is established according to the Emory business, security and compliance practices. Access to the Emory AWS Console must be authenticated with Emory Single sign-on. The virtual private cloud within the environment is protected by the Emory firewall. Secured connection (SSH or RDP) to an EC2 instance must be made from a workstation already located on the Emory network or via a VPN tunnel that is authenticated by 2-factor authentication. All AWS services have been reviewed by the Emory Security Team, and specific guidelines about utilizing these services for HIPAA or identifiable health information will be published. Emory University provides access to the Emory AWS environment to researchers as part of the overall IT support for research. AWS computing and data storage expenses, however, are not covered by the university, and must be budgeted for in grant applications. The EICC works with LITS to provide guidance on AWS usage and optimization.

Computational Services: We divide computational services into two main categories. The first enables expert users to access existing pipelines or develop their own custom analyses. The second category provides investigators the ability to have analyses performed by an EICC computational/bioinformatics expert for a set fee per project. Galaxy provides a wide variety of bioinformatic tools that allow the analysis, manipulation and visualization of large genome-wide datasets from a wide variety of platforms, including microarrays and next-generation sequencing instruments. The EICC also supports an enterprise HIPAA compliant LabKey server for Emory investigators. Collaborators outside Emory can also access this LabKey server infrastructure when collaborating with Emory investigators. PBNAS is a low-cost data storage service offered by EICC.

Standard analysis pipelines using other open-source software packages are implemented for DNA/RNA-seq/ChIP-seq/16S microbiome sequencing projects for human, animal, and microbial genomes. We have implemented the QIIME 2 pipeline for microbiome data analyses. Custom tools or other pipelines (such as mothur) are also available. For the analysis of RNA-seq data, we have implemented the Star and HTseq-count pipeline. Custom tools and pipelines can be developed for specialized projects such as fusion transcript detection. For targeted sequencing, exome sequencing, and whole genome sequencing, we use a custom PEMapper and PECaller pipeline. For variant annotation, we use the bystro.io software package. We have also implemented and analyze data sets with other mapping and variant identification pipelines (BWA, GATK). Substantial capacity exists for these integrated computing resources to support computational/bioinformatic analyses for EICC users.

FACILITIES & OTHER RESOURCES

Updated 1 July 2022

Fields Relevant for the Emory Integrated Metabolomics and Lipidomics Core (EIMLC)

The Emory Integrated Metabolomics and Lipidomics Core (EIMLC), one of the Emory Integrated Core Facilities (EICF) performs quantitative metabolomics and lipidomics analyses on samples from a wide variety of biological matrices (e.g. blood, serum, plasma, solid tissues, cell extracts, etc.) to support both clinical and basic research efforts on campus and in the broader research community. These analyses provide insights into lipids and lipid precursors whose abundance can be monitored as biomarkers to predict and follow progression of a wide range of diseases, such as metabolic disorders (e.g. obesity, type II diabetes, and NAFLD), neurodegenerative diseases (e.g. Alzheimer’s Disease and Parkinson’s Disease), and cancer (e.g. prostate and breast cancer). In addition to lipidomics assays, EILMC capabilities also include targeted and untargeted metabolomics as well as quantitative, plate-based metabolomics, Biocrates Quant500.

The EIMLC is located in Rms. 4075, 4071, G240 and G241 in O. Wayne Rollins Research Center and has 1125 square feet of dedicated wet-lab space. The EIMLC also has a 240 sq ft dedicated office adjacent to the laboratory space on the 4th floor of the O. Wayne Rollins Research Center, which provides space for computational services and customer consultations.

The EIMLC lab houses a Sciex QTrap5500 enhanced high performance hybrid triple quadrupole/linear ion trap LC/MS/MS mass spectrometer with mass range of m/z 5 to 1250 in triple quadrupole mode, and 5-1000 in LIT mode. For high resolution mass spectrometry, the EIMLC utilizes a Thermo ID-X tribrid mass spectrometer that boasts resolution up to 500,000 FWHM and scan speeds up to 30Hz.  Both mass spectrometers feature linear ion traps, permitting MSⁿ studies that aid in the unambiguous characterization of low abundance species. Each mass spectrometer is paired with a complimenting HPLC/UHPLC - the ExionLC AC HPLC/UHPLC system and Vanquish UHPLC, respectively. Data analysis is done using a 44 core Xenon workstation with 196 GB of RAM for processing large datasets. Computer workstations with lipid processing software, such as LipidView (Sciex), MultiQuant (Sciex), LipidSearch (Thermo), and Compound Discover (Thermo), are also available. Minor equipment includes -80 °C freezers, nitrogen evaporators, Biotge Extrahera; a robotic SPE instrument for fully automated specialized lipid extractions, a table top centrifuge, a fume hood, rockers, analytical balances, and multisample vortexers. The EIMLC has computers networked locally with internet-accessible ethernet lines and to a dedicated 24 Tb backup drive (Synology DiskStation). The EILC office is outfitted with three Dell OptiPlex 9020 computers with dual 24” monitors for data processing and 1TB external storage for local backup.                                                       

                                                                                                       MAJOR EQUIPMENT

                                                                                                Updated 1 July 2022

Major Equipment for Emory Integrated Metabolomics and Lipidomics Core (EIMLC) Users

EMORY INTEGRATED METABOLOMICS AND LIPIDOMICS CORE (EIMLC)

The Emory Integrated Metabolomics and Lipidomics Core (EIMLC), one of the Emory Integrated Core Facilities (EICF), performs quantitative metabolomics and lipidomics analyses on samples from a wide variety of biological matrices (e.g. blood, serum, plasma, solid tissues, cell extracts, etc.) to support both clinical and basic research efforts on campus and in the broader research community. Major equipment available in the EIMLC includes:

Sample Preparation:

Omni BeadRuptor: Sample preparation instrument used to grind, lyse, and homogenize samples. This automated, bead mill homogenizer is able to prepare biological samples, including brain, liver, heart, skeletal muscle, adipose, as well as cell culture for lipid or metabolite extraction.

Biotage Extrahera Solid Phase Extraction Robot: This instrument is a robust and automated liquid handling instrument that performs solid phase liquid extractions in both single cassette and 96-well plate formats.

Chromatography:

Sciex Exion LC U/HPLC: Front end liquid chromatography instrument with dual pumping system capable of gradients up to 3ml/min at 6600 bar (9500 PSI).  Instrument contains a cooled autosampler that accommodates two 96 well plates or 105 vials. Used in combination with Sciex Qtrap5500.

1290 Infinity II HPLC: Powerful front end liquid chromatography system capable of 1300bar pressures at 5ml/min. Contains a binary pumping system and chilled autosampler. Used in tandem with Agilent 6495c.

Thermo Vanquish UPLC: High end UHPLC instrument capable of pressures up to 1500 bar at flow rates of 5ml/min. System contains a binary pump and refrigerated autosampler with excellent precision, accuracy, and short cycle times. For use with Thermo IDX hybrid mass spectrometer.

Mass Spectrometers:

Sciex QTrap 5500: Hybrid mass spectrometer with triple quadrupole and linear ion trap, capable of MSn experiments. Instrument has a mass range of m/z 5-1250 and a dynamic range of up to 6 orders of magnitude. Used for targeted lipidomics experiments. 

Agilent 6495c: Advanced, high sensitivity triple quadrupole mass spectrometer with jet ion source permitting 5x more ionization than traditional sources, increasing analytical sensitivity. Mass range of m/z 5-3000 and wide dynamic range. Used for MRM based targeted lipidomics experiments.

Thermo ID-X Tribrid: Hybrid Orbitrap mass spectrometer offering resolution up to 500,000 FWHM in mass range of m/z 50-2000. Contains a linear ion trap capable of MSn scans at 40Hz. Used for ultra high resolution untargeted, global lipidomics as well as metabolomics.

Software:

Analyst 1.5: Used for the operation of QTrap5500 mass spectrometer and collection and processing of targeted lipidomics data.

LipidView: Software used for the identification of lipids in biological samples by searching parent and fragment ion masses to a proprietary database containing over 25,000 lipids in a wide variety of lipid classes.

MultiQuant: Modular software used for processing MRM based datasets. Uses algorithms optimized for the automated integration of peaks with low signal to noise ratios.

MassHunter: Software used for the operation and analysis of mass spectrometry data collected on the Agilent 6495c.

Excalibur: Used for the operation of Thermo IDX mass spectrometer. Contains modules for the processing and analysis of mass spectrometry data.

LipidSearch: Lipid identification software that searching fragment ion data against a proprietary database to streamline identification of lipid species and visualization of data.

Compound Discoverer: Software that streamlines identification of small molecules by searching full scan and MSn data with known compounds and molecular pathways.

FACILITIES & OTHER RESOURCES

Updated: September 1, 2020

Fields Relevant for Emory Integrated Proteomics Core (EIPC) Users

EMORY INTEGRATED PROTEOMICS CORE (EIPC)

The Emory Integrated Proteomics Core (EIPC), one of the Emory Integrated Core Facilities (EICF), provides protein analytical services by cutting-edge mass spectrometry (MS). The EIPC has 200 sq ft of dedicated office adjacent to the 1500sq ft laboratory space on the 5th floor of the Whitehead Biomedical Research Building, which provides for computational services, meeting customers, and weekly EIPC team meetings.

The EIPC houses several mass spectrometers—hybrid quadrupole-orbitrap including a Q-Exactive, and a Q-Exactive HF-X; tribrid mass spectrometers including two Orbitrap Fusion, and an Orbitrap Fusion Lumos; and a TSQ Altis triple-stage quadrupole (see major equipment). Each instrument is coupled with an autosampler and HPLC system. The system allows automated capillary LC-MS/MS runs for top-down, middle-down and bottom-up analyses with high resolution. These mass spectrometers are capable of detecting peptides at subfemtomolar level, identifying hundreds to thousands of proteins in complex mixtures, mapping posttranslational modification sites, and quantifying proteins based on label-free methods or different labeling strategies (e.g. TMT and SILAC). The nanoACQUITY UltraPerformance LC System is designed for nanoscale, capillary, and narrow-bore separations to attain the highest chromatographic resolution, sensitivity, and reproducibility. Both qualitative and quantitative projects benefit from the added pressure capacity (up to 10,000 psi); sensitivity is increased several folds with the use of sub-2 µm chromatographic resins and retention time reproducibility enables label-free quantitative approaches. The core has also established the electrostatic repulsion hydrophilic interaction chromatography (ERLIC) that uses both hydrophilic interaction and electrostatic forces on an Agilent 1100 HPLC.

The computational platform is capable of performing sophisticated data analyses, including database search (i.e. matching MS/MS spectra to peptide sequences), data filtering (i.e. removing false positive matches), statistical inference, as well as data storage, presentation and distribution. EIPC has multiple search engine platforms including Sequest, Mascot, and Byonics. A Sage-N Sorcerer2 IDA is located in-house and currently runs Sorcerer Sequest and Scaffold. The Mascot, Proteome Discoverer 2.0, and Byonic platforms are licensed on a computing cluster in collaboration with the Emory Integrated Computing Core. Numerous computational tools have also been developed for high throughput data processing. All personnel have access to high-end workstations capable of processing both raw and post-analyzed data.                                                                                      

MAJOR EQUIPMENT

Updated: September 1, 2020

Major Equipment for Emory Integrated Proteomics Core (EIPC) Users

EMORY INTEGRATED PROTEOMICS CORE (EIPC)

Q Exactive Plus Hybrid Quadrupole-Orbitrap Mass Spectrometer (Thermo Fisher Scientific): The Q Exactive Plus Orbitrap is coupled to an autosampler and nanoAcquity UPLC system. This instrument features high ion currents because of an S-lens, and fast high-energy collision-induced dissociation (HCD) peptide fragmentation because of parallel filling and detection modes. The image current from the detector is processed by an “enhanced Fourier Transformation” algorithm, enabling high mass spectrometric resolution (up to 140,000 FWHM). With almost instantaneous isolation and fragmentation, the instrument can sequence 10 peptides per second. This instrument is also capable of proteomics approach termed parallel reaction monitoring (PRM), which is a targeted proteomics strategy wherein all product ions of a peptide are simultaneously co-detected under conditions that offer high resolution and high mass accuracy.

Q Exactive HF-X Hybrid Quadrupole-Orbitrap mass spectrometer (Thermo Fisher Scientific): The Q Exactive HF-X mass spectrometer harbors a high-field (HF) Orbitrap mass analyzer and an Advanced Quadrupole Technology (AQT) resulting in higher resolution (240,000 at m/z 200) and scan speed (up to 40 Hz). A High Capacity Transfer Tube (HCTT) and electrodynamic ion funnel also contributes towards the improved sensitivity of the instrument. This mass spectrometer enables fast identification and analysis of peptides, label-free and TMT quantitation. An EASY-nLC™ 1200 system is connected with the mass spectrometer for peptide separation.

Orbitrap Fusion Tribrid Mass Spectrometer (Thermo Fisher Scientific): The fusion is an Orbitrap hybrid mass spectrometer and is coupled to an UltiMate 3000 RSLCnano system. The Fusion is equipped with a mass filter, a collision cell, a high-field Orbitrap analyzer, and, finally, a dual cell linear ion trap analyzer (Q-OT-qIT). This system offers high MS/MS acquisition speed of 20 Hz and detects up to 19 peptides sequences within a single second of operation. The Fusion also has resolution in excess of 450,000 allowing for separation of isobaric interferences.

Orbitrap Fusion Tribrid Mass Spectrometer with Electron Transfer Dissociation (ETD) (Thermo Fisher Scientific): The fusion is an Orbitrap hybrid mass spectrometer, which is coupled to an UltiMate 3000 RSLCnano system. The Fusion is equipped with a mass filter, a collision cell, a high-field Orbitrap analyzer, and, finally, a dual cell linear ion trap analyzer (Q-OT-qIT). This system offers high MS/MS acquisition speed of 20 Hz and detects up to 19 peptides sequences within a single second of operation. The Fusion also has resolution in excess of 450,000 allowing for separation of isobaric interferences. This Fusion is also equipped with Electron Transfer Dissociation (ETD), which is an orthogonal fragmentation technique to HCD and collision induced dissociation (CID), which will enhance peptide identification and localization of labile post-translational modifications (PTMs), such as glycosylation and phosphorylation.

Orbitrap Fusion Lumos Mass Spectrometer with Electron Transfer Dissociation (ETD) (Thermo Fisher Scientific): The Fusion Lumos mass spectrometer has three mass analyzers— quadrupole, orbitrap, and linear ion trap— as in the fusion tribrid system. The instrument houses an upgraded ion optics (High Capacity Transfer Tube and Electrodynamic Ion Funnel), an Advanced Quadrupole Technology (AQT), and a new ETD-HD feature. The MS/MS acquisition rates of Lumos is up to 20 Hz for both Orbitrap and linear ion trap measurements. Ultra-high-field Orbitrap mass analyzer increases the resolving power up to 500,000 FWHM at m/z 200. Synchronous Precursor Selection (SPS) feature significantly augments the number of peptides and proteins identified and improves quantitative accuracy in TMT experiments. This feature is also available in other Fusion instruments. Lumos offers several fragmentation modes, like CID, HCD, ETD, and EThcD, that are helpful for PTM analysis. Lumos is connected to an EASY-nLC™ 1200 system for UHPLC.

TSQ Altis triple-stage quadrupole mass spectrometer (Thermo Fisher Scientific): The TSQ Altis is a triple-stage quadrupole mass spectrometer fitted with segmented quadrupoles with hyperbolic faces provides ultra-high sensitivity (0.2 Da FWHM) for high resolution selected reaction monitoring (H-SRM). Additionally, the active collision cell with axial DC field facilitates fast selected reaction monitoring (up to 600 SRMs/sec). This instrument is suitable for the quantitation of low-level compounds in complex biological matrices. The mass spectrometer is coupled to a Waters nanoAcquity UPLC system.

UltiMate 3000 RSLCnano (Thermo Fisher Scientific): UltiMate 3000 RSLCnano system can be operated with nano-, capillary-, and micro-flow options. ProFlow technology in this system improves nano flow rate control resulting in high retention time precision that is crucial for LC-MS based proteomics methodology. The pressure capacity of this UHPLC is up to 860 bar (12473 psi).

nanoAcquity UPLC (Waters Corporation): The nanoACQUITY UltraPerformance LC System is designed for nano-scale, capillary, and narrow-bore separations to attain the highest chromatographic resolution, sensitivity, and reproducibility. Both qualitative and quantitative projects benefit from the added pressure capacity (up to 10, 000 psi); sensitivity is increased several folds with the use of sub-2 μm chromatographic resins and retention time reproducibility enables label-free quantitative approaches.

EASY-nLC 1200 System (Thermo Fisher Scientific): EASY-nLC 1200 System is a capillary UHPLC system that allows for a maximum backpressure up to 1200 bar (17,404 psi). This higher pressure allowance increases the peak capacity resulting in better peptide separation and increased throughput.

Liquid Handling Station (LHS): The BRAND Liquid Handling Station handles routine pipetting tasks (e.g., BCA assay, protein digestion, aliquoting, etc.) at high speed and with the highest precision.

Off-line Liquid Chromatography systems (Agilent Technologies): An Agilent 1100 series system comprising of a degasser, binary pump, autosampler, UV-detector and a fraction collector is available for offline fractionation of samples. The system is capable to handling all current fractionation methods including high-pH reverse phase, SCX and ERLIC.

Computing: The Emory Integrated Proteomics Core (EIPC) has multiple search engine platforms including Sequest, Mascot, and Byonics. A Sage-N Sorcerer2 IDA is located in-house and currently runs SorcererSequest and Scaffold.  The Mascot, Proteome Discoverer 2.0, and Byonic platforms are licensed on a computing cluster in collaboration with the Emory Integrated Computational Core (EICC). Core facility personnel have access to high-end workstations capable of processing both raw and post-analyzed data.

Shared equipment: Includes gel imagers for chemiluminescence and fluorescence, equipment for protein, a LiCor fluorescent system for quantitative immunoblotting. Fluorescence and standard microplate readers are available for protein quantification. High-speed and ultra-centrifuges are available as core equipment. There are sliding microtomes, standard and dual beam spectrophotometers, cryostats, pH meters, balances, oven, refrigerators, hot plates, stirrers, -70C freezers, and other standard equipment.

Facilities and Resources

Updated: 1 July 2022

Fields Relevant for Emory Multiplexed Immunoassay Core (EMIC) Users

EMORY MULTIPLEXED IMMUNOASSAY CORE (EMIC)

The Emory Multiplexed Immunoassay Core (EMIC), one of the Emory Integrated Core Facilities (EICF) uses the multiplexed immunoassays to bring a powerful research platform to help investigators from Emory University and external researchers. The EMIC is located in a laboratory 665E on the 6th floor of the Whitehead Biomedical Research Building. The EMIC performs and analyzes multiplex immunoassays to measure the levels of single or multiple targets within a single, small volume sample on the Meso Scale Discovery (MSD) platform.  EMIC houses two high-sensitive imaging detection system Meso Scale Discovery SECTOR2400 and Quickplex SQ120. MSD uses electrochemiluminescence via a cooled scientific-grade CCD camera to detect binding events with a broad dynamic range and exceptional sensitivity(pg/ml). MSD supports a wide variety of assays from different research area: immunology, neurobiology, oncology, toxicology, cardiovascular, metabolic etc. MSD measures protein levels in many biological matrices (plasma, serum, CSF, urine, stool tissues, etc).

The EMIC houses two plate readers (SECTOR2400 and QuickPlex SQ120) to meet the needs of its users. These instruments require no customer calibration or maintenance, no complicated fluidics, and no between-read cleaning. The combination of rapid read times (90 seconds per plate) and the ability to perform multiple, simultaneous tests on a single sample increases productivity, conserves sample, and delivers results quickly. The MSD platform has a wide variety of commercially available assay kits and a full line of components and reagents for developing customized assays.

MAJOR EQUIPMENT

Updated 1 July 2022

Major Equipment for Emory Multiplexed Immunoassay Core (EMIC) Users

EMORY MULTIPLEXED IMMUNOASSAY CORE (EMIC)

The Emory Multiplexed Immunoassay Core (EMIC), one of the Emory Integrated Core Facilities (EICF), houses two plate readers (SECTOR2400 and QuickPlex SQ120) to meet the needs of its users. These instruments require no customer calibration or maintenance, no complicated fluidics, and no between-read cleaning. The combination of rapid read times (90 seconds per plate) and the ability to perform multiple, simultaneous tests on a single sample increases productivity, conserves sample, and delivers results quickly. The MSD platform has a wide variety of commercially available assay kits and a full line of components and reagents for developing customized assays.

One high sensitivity imaging detection system SECTOR2400: provide unparalleled sensitivity and dynamic range, simple protocols, rapid and continuous reads, and fast, well-organized results via DISCOVERY WORKBENCH assay analysis software.

One high sensitivity imaging detection system MESO QuickPlex SQ 120: provide unparalleled sensitivity and dynamic range, simple protocols, rapid and continuous reads, and fast, well-organized results via DISCOVERY WORKBENCH assay analysis software.

Emory Cellular and Immunotherapy Core (ExCITE) - FACILITIES & OTHER RESOURCES

FACILITIES & OTHER RESOURCES

Updated: June 14, 2022

Specific Fields Relevant for Emory Cellular and Immunotherapy Core (ExCITE) Users

EMORY CELLULAR AND IMMUNOTHERAPY CORE (ExCITE)

The Emory Cellular and Immunotherapy Core (ExCITE) is one of the Emory Integrated Core Facilities (EICF).  This fee for service laboratory is a clinical cell manufacturing facility that prepares cellular and immunotherapy products under current Good Manufacturing Practices (GMP) for the development investigational new drugs and diagnostics methods. The central mission of the lab is to provide GMP-compliant cell manufacturing and/or consultation for the translational of Emory-based or external research collaborations into early phase clinical trials. The types of products routinely handled by ExCITE include autologous and allogeneic mesenchymal stem cells, apheresis products, including transduced lymphocytes, red blood cells (RBCs) and cardiomyocytes. Standard processes performed by ExCITE include isolation, expansion, and cryopreservation of mesenchymal stem/stromal cells, dendritic cells, transduction and or transfection of lymphocytes and other cellular products for investigational new FDA-sanctioned studies.

The ExCITE lab is accredited by the Foundation for the Accreditation of Cellular Therapy (FACT) for more than minimally manipulated cellular therapy products as well as College of Pathologist (CAP) certification. There are four laminar flow hoods (Nuaire), 8 CO2 incubators, two swinging bucket temperature-controlled centrifuges, a suite of Miltenyi CAR (chimeric antigen receptor) production equipment (MACSQuant, Prodigy), mycoplasma and endotoxin detection, an ISBT label printer and computer equipment as needed all located within our space. Future plans are in place to double the lab’s capacity with the addition of another 2 iSO7 rooms. The ExCITE lab has a dedicated office on the same floor as the laboratory space on the 4th floor of the University Hospital Tower, which provides for computational services, meeting customers, and ExCITE team meetings. Additionally we have meeting rooms available on Clinic B, level 3.

MAJOR EQUIPMENT

Updated 1 September 2020

Specific Fields Relevant for Emory Cellular and Immunotherapy Core (ExCITE) Users

EMORY CELLULAR AND IMMUNOTHERAPY CORE (ExCITE)

The Emory Cellular and Immunotherapy Core (ExCITE), one of the Emory Integrated Core Facilities (EICF), is a 300 square feet ISO7 clean room located on the 5th floor of the Emory University Hospital with dedicated space for GMP compliant cell processing. Two laminar flow hoods (Nuaire) and 6 CO2 incubators are also located within the space. The infrastructure includes equipment necessary for cell processing including a Cobe 2991 cell washer, a centrifuge, a light microscope and phase microscope, rocking platforms, digital vortex mixer and sealers. Other specific equipment include:

Sysmex XE-2100L: The Sysmex XE-2100L Analyzer is a quantitative automated hematology analyzer for in vitro diagnostic use in clinical laboratory for determining hematological parameters such as WBC, RBC’s, nucleated RBC’s, HCT, HG, immature cells scattergram, pattern data of cell size distribution curves for platelet, 23 analysis parameters, and research data of 4 parameters.

Aero Trak-9510: Aero Trak-9510 Airborne Particle Counter is an instrument that detects and counts physical particles present in the air. Aerosol particle counters are used to determine the air quality by counting and sizing the number of particles in the air. This information is useful in determining the amount of particles inside a building or in the ambient air. It is also useful in understanding the cleaning level in a controlled environment such as a cleanroom.

CliniMACS Plus: CliniMACS Plus instrument is an automated cell separation system based on MACS technology. It enables the operator to perform clinical scale magnetic enrichment of target cells or depletion of unwanted cells in a closed and sterile system.

Cellometer Auto2000: A digital cell counter and viability instrument.

Equipment located outside the GMP space:

Flow Cytometry: The ExCITE has a dedicated 8-color FACS Canto II Flow Cytometer that have automated loading racks to facilitate high through-put analyses of samples.

Additional ExCITE equipment include: 1 biologic safety cabinet, -20 and -80 C freezers, ELISA plate washer and reader.

Facilities and Resources

Fields Relevant for the Emory Stem Cell Core (ESCC)

Updated: 1 July 2022

The Emory Stem Cell Core (ESCC), one of the Emory Integrated Core Facilities (EICF), brings a powerful research platform of generating patient specific stem cells and neural progenitor cells in support of Emory investigators. The ESCC’s focus and technical expertise is to derive and characterize human induced pluripotent stem cells (iPSCs) from terminally differentiated somatic cells using non-integrating methods. IPSCs generated from patients with a genetic defect allows for a unique opportunity to study the mechanisms of disease in an in vitro model. Other applications for these cells include CRISPR gene editing the cell lines, developing a reporter line, drug screening and discovery, and potentially regenerative therapies. Additionally, the core will provide training and educational resources to support investigators with interest in human stem cells. The ESCC interfaces with other members of the Emory Integrated Core Facilities as a pipeline to analyze patient cells that will inform drug discovery and personalized medicine.

The ESCC uses human cells, whole blood and skin samples, as provided by investigators with IRB approval, as source material for the derivation of an induced pluripotent stem cell (iPS) line. The ESCC is able to isolate primary fibroblasts from skin tissue and acquire a variety subtypes of blood cells from whole blood. Patient LCLs and iPS-derived neural progenitor cells can also be generated by the core. Additionally, established human iPS, embryonic stem cell lines, LCLs, HEK293T cells and other various established cell lines are cultured in the lab.

The ESCC located in a laboratory located on the 4th floor of the Whitehead Biomedical Research Building, with approximately 200 square feet of dedicated cell culture and wet-lab space. The ESCC’s cell culture room includes two biosafety cabinets, four carbon-dioxide incubators, two EVOS microscopes, a Countess cell counter, a Neon transfection system and a PCR machine. The ESCC also houses its own LS6000 liquid nitrogen dewar with a CS100 controller for automatic level control for storage of cryopreserved cells during active projects. The ESCC has additional access to a Nikon Eclipse TI Fluorescence Microscope, a Nikon Biostation IM Microscope, a Keyence Fluorescence Microscope, an Applied Biosystems QuantiStudio 6 Flex Real Time PCR machine, a Biorad ChemiDoc MP Imaging system and a Synergy H1 Multi-mode Plate Reader.

MAJOR EQUIPMENT 

Major Equipment for ESCC Users

Updated: 1 July 2022

Emory Stem Cell Core (ESCC) is located in a laboratory located on the 4th floor of the Whitehead Biomedical Research Building, with approximately 200 square feet of dedicated cell culture and wet-lab space and 200 square feet of office space. The ESCC infrastructure includes:

Two ThermoFisher 1300 Series Class II biosafety hoods. The 4 feet safety cabinets provide superior protection for daily culturing of cells with SmartFlow design with digital airflow verification and adjust airflow as filter resistance changes. The installed UV light works as an effective germicide and viricide for daily use.

Four HERACELL VIOS 160I CO2 incubators. These CO₂ incubators support a range of culturing needs for optimal cell growth. In-chamber fan gently distributes clean, humidified air throughout the chamber ensuring homogeneous conditions and fast recovery of all parameters in 10 minutes or less for stable culturing conditions. The In-chamber HEPA continuously filters the entire chamber air volume every 60 seconds and the steri-run sterilization feature ensures elimination of all biological contaminants.

Two EVOS XL Core microscopes. The EVOS®XL Core Imaging System is a digital, transmitted light, inverted imaging system for cell and tissue culture applications and routine cell maintenance. These compact systems are kept inside the biosafety cabinets and allow for routine imaging of cells without the worry of contamination from exposure to the environment outside the cabinet. The large LCD screens allow for multiple user viewing and are excellent for training and teaching.

Worthington LS6000 liquid nitrogen dewar with CS100 Automatic Controller. A liquid nitrogen refrigeration system that holds nearly 5000 2 ml cryovials for cryogenic storage of cells. The CS100 controller is a sophisticated automatic level controller that provides standard alarms and stores more than 500,000 events.

ThermoFisher Sovall ST16 centrifuge. A benchtop machine to perform cell culture and blood processing applications with a variety of rotors for 15 ml tubes, 50 ml tubes and microcentrifuge tubes.

Fisher ISOtemo waterbath. A water bath that allows for consistent temperatures and reliability for routine culturing purposes.

Applied Biosystems Countess II FL. A benchtop cell counter equipped with state-of-the-art optics, full autofocus, and image analysis software for rapid assessment of cells in suspension. It comes with three-channel flexibility (brightfield and two optional fluorescence channels) to count cells, monitor fluorescent protein expression, evaluate apoptosis, and measure cell viability.

Invitrogen Qubit Fluorometer. A fluorometer designed to accurately measure DNA, RNA, and protein quantity in less than 3 seconds per sample with high levels of accuracy using only 1-20 ul of sample.

Applied Biosystems SimpliAmp Thermal Cycler. A compact 96 well thermal cycler for essential PCR flow and a veriflex temperature control for 3 zones  with accurate optimization.

Invitrogen E-gel iBase and Safe Imager Electrophoresis system. A electrophoresis system allows for the separation of DNA in 7 minutes and the  transilluminator that allows real-time visualization of the migration of  the DNA in the e-gels. This system replaces the need for staining with ethidium bromide and visualization using UV making it a much safer and more effective way to visualize DNA.

Invitrogen Neon Transfection System. A transfection machine that enables fast and efficient delivery of nucleic acids into all mammalian cell types including primary and stem cells. Unlike standard cuvette-based electroporation chambers, the neon uses biologically compatible pipette tip chamber that generates a more uniform electric field in 10 or 100 ul reactions.

Additional Equipment Access to:

Nikon Eclipse TI Fluorescence Microscope. An inverted motorized microscope for fluorescence imaging of live or fixed cells on slides.

Nikon Biostation IM Microscope. A live cell imaging system that incorporates a microscope, an incubator and CCD camera to provide a stable environment for live cells imaging and simple long term time lapse data acquisition.

Keyence Fluorescence Microscope. A benchtop microscope that captures high-resolution publication quality images without the necessity of a dark room. It accommodates brightfield, fluorescence, and phase contrast observation with a single unit. It supports slides, cell-plates, dishes, and flasks for imaging different samples.

Applied Biosystems QuantiStudio 6 Flex Real Time PCR system. A real time PCR machine with a 96 well block for assays for gene expression, genetic variation, gene regulation, or protein expression experiments.

Biorad  ChemiDoc MP Imaging System. A full feature instrument for imaging and analyzing gels and western blots. It is designed for multiplex fluorescent western blotting, chemiluminescence detection, general gel documentation and stain-free imaging.

Synergy H1 Hybrid Multi-Mode Reader. Synergy™ H1 is a configurable multi-mode microplate reader, with monochromator-based optics for flexibility, filter-based optics for sensitivity, or both. BioTek’s patented Hybrid Technology™ offers applications versatility and excellent performance in a modular platform to expand as your laboratory’s needs change. Synergy H1 now offers continuously variable bandwidth monochromators for fluorescence excitation and emission wavelength selection; the fluorescence bandwidth can be set between 9 nm and 50 nm, in 1 nm increments, allowing users to fully optimize reader settings to drive the best assay performance compared to fixed bandwidth systems.

FACILITIES & OTHER RESOURCES

Updated: April 2023

Fields Relevant for the Integrated Cellular Imaging Core (ICI) Users

INTEGRATED CELLULAR IMAGING CORE (ICI)

The Integrated Cellular Imaging Core (ICI), one of the Emory Integrated Core Facilities (EICF), is housed in five main locations within the central research and clinical area of Emory’s campus the ICI hosts 21 microscopes and 5 workstations in approx. 3400 sq ft of scope room, wet space, and bench space.  Each location requires either keycard or physical key entry to ensure only ICI trained users have access to the equipment. Each location has available wet space for basic preparations, in addition to being located within close proximity to multiple lab spaces, allowing for easy access to researchers own preparation areas. We house 21 different microscopes ranging from basic widefield setups to the more advanced and cutting edge.  These include confocal, spinning disk, multiphoton, super-resolution (SIM and STED), and light sheet (including a 3i lattice light sheet and Miltenyi Blaze LFOV), with 13 systems (including at least from each modality) equipped for live cell conditions.

Service: The ICI team assists researchers with fluorescence experiments from an extremely broad range of scientific areas, from physics and chemistry to basic biology and translational research. Services range from experimental education and consultations, assisting and advising on sample prep, to optimizing data acquisition and subsequent analyses. The ICI supports investigators from start to finish, from bench to publication, at any point that assistance is needed. While using the microscope is the central part of our process, we are keenly aware that pre- and post-acquisition are equally important and are strongly emphasized during consultations. We help mold scientific questions to the right microscope, data set and analysis, and ultimately to researchers’ answers.

Data Collection, Management, and Analysis: All microscope acquisition data is automatically synced each night to an Emory Library and Information Technology Services (LITS) server to ensure redundancy. Data analysis can then be performed on either user located machines or ICI workstation locations. We advise, assist, and train users with data access and quantitative analyses as required. In addition to standard analysis and 3D visualizations, we provide custom Fiji macros and plugins, Imaris XTensions, and video sequencing (see NoPhotonLeftBehind YouTube channel).

Education: ICI holds periodic educational seminars and journal clubs. To advance our educational mission beyond the walls, we have a range of bite-sized YouTube tutorials on simple data analyses for Fiji, CellProfiler and Imaris, viewed by over 150k views and approaching 600 subscribers.

ICI Technical Support Team:

Adam Marcus, PhD – ICI Scientific Director

Dr. Marcus is an Winship 5K Research Professor in the Department of Hematology and Medical Oncology at Emory University School of Medicine. Dr. Marcus serves as Deputy Director for Winship Cancer Institute of Emory University, leading the integration of the research, clinical, and educational components within Winship Cancer Institute of Emory University. He also serves as Associate Vice President for Research in Emory University's Woodruff Health Sciences Center, and Associate Dean for Novel Technology and Research Cores leading the Emory Integrated Core Facilities and Division of Animal Resources. He provides strategic and operational oversight as well as scientific direction for the Emory Integrated Core Facilities. Marcus is also Scientific Director of the Emory Integrated Cell Imaging Core (ICI), a jointly managed shared resource of Winship Cancer Institute and Emory University School of Medicine. His laboratory has been focused on the cell and molecular biology of lung cancer invasion for the last 14 years. In particular, investigating how cells invade into 3-D microenvironments using a combination of live cell imaging approaches, 3D models, and standard molecular biology. Dr. Marcus developed and applies an image-guided genomics technique termed spatiotemporal genomic and cellular analysis (SaGA), utilizing photoactivated cell-specific selection for probing the biology of phenotypically heterogenous cells within a larger cancer cell population. In addition, Dr. Marcus’ lab is focused on STEM based learning in Georgia schools. In this role, he co-directs a 5-year NIH-funded, K-12 STEM outreach program (citizensciencehd.com) to promote diversity in STEM. This establishes a unique Citizen Science based curriculum in Georgia schools and has a full evaluation and outcomes component.

Laura Fox-Goharioon – ICI Core Director

Ms. Fox-Goharioon is the Director and reports directly to the Assistant Dean of Research and the oversight committee for the ICI. She is an experienced microscopist with over 37 years of cell biology and imaging experience at Emory University at the Whitehead location. She has over 13 publications focused on cell biology and imaging and has taken courses in super-resolution imaging and advanced image analysis, including the Analytical and Quantitative Light Microscopy course in Woods Hole, MA. She joined ICI at its inception and directly oversees the day-to-day operations of the core as well as six microscopes including live cell, confocal, super resolution, and multiphoton imaging.

April Reedy, PhD – ICI Assistant Scientist

Dr. Reedy is an Assistant Scientist with the School of Medicine with 15 years of applied microscopy experience in genetics and molecular biology, developmental biology and model systems. In her PhD in genetics and molecular biology she made numerous discoveries into the pathophysiology of Duchenne’s Muscular Dystrophy (DMD) in C. elegans. She has advanced confocal experience applied to C. elegans and Drosophila, including electrophysiology-based calcium imaging and ratiometric ROS imaging. Dr. Reedy also has immunofluorescence, pathology-based immunohistochemistry, and immuno-EM and cryo-sectioning experience. In addition to her extensive applied microscopy experience, Dr. Reedy has become a huge resource to investigators regarding experimental design.

Austin Worden, PhD – ICI Assistant Scientist 

Dr. Worden is a Biomedical Scientist who completed his graduate work at the University of South Carolina School of Medicine, utilizing multiple forms of microscopy in his work. He first received his master’s degree concentrated in applied biotechnology where he worked on the creation of a novel three-dimensional cell culture model for the analysis of cellular interactions. He then completed his PhD concentrated in cellular and molecular biology where he focused on the role of the microenvironment in the molecular signaling of adipose-derived stem cells with implications in regenerative medicine, early embryonic development, and cancer metastasis.  Austin has taught both undergraduate and graduate level courses as a teaching assistant, including a graduate microscopic analysis course. He has always been fascinated by microscopes and the microanalysis of the everyday world.

Stoyan Ivanov, M.Sc. – ICI Research Specialist

Mr. Ivanov is a Physicist who completed his undergraduate and master’s degrees at the Georgia Institute of Technology. His graduate work focused on the interaction between Mercury’s magnetic field and the incident Solar wind during Coronal Mass Ejections that passed through the near-Mercury environment under Dr. Carol Paty. He studied how these plasma conditions affected the incidence of ion precipitation on the surface and how that relates to surface weathering. Stoyan has had experience in a wide range of fields including radioastronomy at the Jet Propulsion Laboratory, space plasma modeling during his graduate work, and biomedical engineering at Sorrento Therapeutics Inc. He is excited to apply his previous experiences to the cell imaging work of the core, help other researchers with their studies and imaging, and learn a great deal along the way.

Hunter Hakimian, PhD – ICI Assistant Scientist 

Hunter is a Neurobiologist who, after receiving his undergraduate degree in Physics from the Georgia Institute of Technology in Atlanta, received his PhD at the University of Florida in the J Crayton Pruitt Family Department of Biomedical Engineering in the Neuroprostheses Research Lab under Kevin J. Otto as well as the Department of Pathology under Clive Wasserfall where he studied novel intracortical microstimulation techniques and the persistence of single beta cells in type 1 diabetes patients, for which he employed automated computer vision techniques and big data processing. He also made use of big data techniques for the UF HuBMAP chapter, where he formatted and uploaded large human microscopy datasets to both UF’s local supercluster and the global HuBMAP Atlas. He has extensive experience with machine learning, cloud data sharing and neural engineering and looks forward to sharing that knowledge in pursuing the development and facilitation of biological research methods with the diverse users of the ICI core.

MAJOR EQUIPMENT

Updated: April 2023

Major Equipment for Integrated Cellular Imaging Core (ICI) Users

INTEGRATED CELLULAR IMAGING CORE (ICI)

The Integrated Cellular Imaging Core (ICI), one of the Emory Integrated Core Facilities (EICF), provides state-of-the-art light microscopy and image analysis platforms. ICI offers confocal, spinning disk confocal and live cell imaging, multi-photon animal and tissue imaging, widefield with deconvolution, super resolution, light sheet and image analysis. To effectively implement these technologies, ICI provides consultations, expert training, and support for all our systems. We assist our users from bench to publication, starting with designing experiments tailored to the specific microscope, through training and data acquisition, to data analysis and interpretation.

Confocal Imaging:

Leica SP8 (Winship): The Leica SP8 confocal laser scanning unit, attached to the latest Leica inverted DMi8 body, comprises an infinitely flexible prism based spectral detector system and multiple excitation laser lines (405, 488, 514, 561 and 633nm) for a vast variety of experimental and labeling options. Four channel detection, via two PMTs and two extremely sensitive Leica HyD detectors (GaAsP based), together with 8 kHz resonant scanning provides high speed imaging. A transmitted light detector allows for simultaneous laser scanned DIC or phase imaging. A stage and objective warmer facilitates numerous live cell imaging approaches such as FRET, FRAP, and photoconversion. High speed automated tiling/stitching and multipoint location acquisitions are also possible in combination with the above.

Olympus FV1000 (HSRB): This FV1000 confocal laser scanning microscope is mounted on an inverted Olympus IX81 microscope with a motorized x-y-z stage. It has a three channel PMT detection system with grating based spectral detectors on channels 1 and 2 (allowing for spectral unmixing). In addition, a transmitted light detector provides laser scanned DIC for label free imaging. These coupled with 6 excitation laser lines (405, 458, 488, 515, 559, and 635nm) facilitate highly flexible imaging combinations.

Olympus FV1000 (Whitehead): This FV1000 laser scanning microscope is identical to the HSRB FV above, except it’s filter based detection on all channels and a different combination of excitation laser lines (405, 488, 515, 543, 635). Having near identical systems in two locations provides easy secondary options without additional trainings during maintenance and repairs.

Live cell confocal imaging:

Nikon A1R HD25 (Whitehead): This live cell confocal laser scanning microscope is optimized for imaging cellular dynamics at high speed and a large view of view (25mm). A hybrid dual scanning confocal system with both galvanometric and resonant scanners, together with a piezo z controller, can acquire 1024x1024 images at 15 fps, 512x512 images at 30 fps, or with a reduced size up to 720 fps. A stage top environmental chamber at 37° C and 5% CO₂ required for live cell imaging, coupled with a Perfect Focus system, provides extremely stable long-term imaging without drift. Flexible laser scanning control for photokinetics experiments can be conducted in multiple user-defined regions of interest. Six laser lines (405, 440, 488, 514, 561, & 640nm) and four channel PMT (2x GaAsP, 2x Multi-Alkali) detectors, in addition to a transmitted light channel for laser scanned DIC provide flexible live cell experimental options. A DUVB-2 GaAsP spectral detector unit provides arbitrary 10 – 320 nm wide spectral windows between 400 and 720 nm for complete spectral flexibility. NIS Elements packaged with analysis options coupled to JOBS tailorable data-based control system.

Nikon Ti2-E – Crest X-Light Spinning Disc Confocal (Winship): A Nikon controlled Eclipse Ti2-E with a CrestOptics X-Light V2 L-FOV ultrafast spinning disk confocal provides a 18mm FOV utilizing a sensitive high speed sCMOS camera (~100fps or more for cropped ROI). A stage top environmental chamber at 37° C and 5% CO₂ required for live cell imaging, coupled with a Perfect Focus system, provides extremely stable long-term imaging without drift. A fast z-piezo and motorized xy stage provides high speed automated multi-location and tiling/stitching acquisitions. Seven laser lines (408, 445, 473, 518, 545, 635, & 750nm), DIC, and phase acquisitions are available. NIS-Elements packaged with analysis options coupled to JOBS enable tailorable data-driven acquisitions.

Leica Stellaris 8 (HSRB II): A point scanning system, including a White Light Laser as excitation light source. An extended detection range up to 850 nm plus the expanded excitation range in the visible from 440 nm up to 790 nm allow the application and separation of an extended range of spectrally overlapping fluorophores, up to five simultaneously. It is equipped with a 405-diode laser as well.  The Stellaris has both Galvano and resonant scanners, 5 detectors, including 3 Power HyD-S and 2 Power HyD-X, a Tokai Hit stage top incubator for CO2 and temperature control, Navigator software for tiling, TauSense for FLIM, and LIGHTNING for optimal extraction of image details and maximum resolution.

Super-resolution imaging:

Nikon N-SIM (Whitehead): The Nikon Structured Illumination Microscope (SIM) doubles the resolution of widefield microscopy in all three dimensions (down to 120 nm x-y and 300 nm z resolution), and can image samples prepared with conventional techniques (same as confocal or widefield). A sensitive iXon EMCCD camera and three laser line system (488, 514, and 561nm) provides high speed multi-color acquisitions. A SIM-TIRF mode is also available. The system also includes a 37°C 5% CO₂ and humidity-controlled stage insert, together with heated objectives for the option of live cell super resolution acquisitions.

Deltavision OMX BLAZE (HSRB I):The DeltaVision OMX imaging platform is an advanced multi-mode, super-resolution microscope system. DeltaVision OMX provides 4 color super-resolution imaging using 3D structured illumination (3D-SIM) as well as ultra-fast widefield-deconvolution acquisition (3x sCMOS cameras for 300 fps imaging). The OMX Blaze also has Ring-TIRF capabilities to image biological processes at the cell surface-coverslip interface. The laser scanning optics of the TIRF beam path allow for fast switching of photoactivation and photokinetics in combination with live cell widefield-deconvolution, 3D-SIM imaging or TIRF. The system also includes 37°C 5% CO₂ and humidity-controlled stage inserts, along with heated objectives for the option of live cell super resolution acquisitions.

3i Lattice Light Sheet (Winship): The Intelligent Imaging Innovations (3i) lattice light sheet microscope (LLSM) is state-of-the-art for rapid high-resolution live cell imaging with low phototoxicity stemming from efficient lightsheet excitation/collection. Compared to a spinning disk confocal, the LLSM features 100x less phototoxicity/photobleaching in dithered mode. The collection objective, a Nikon 25X/1.1NA, is matched with a tube lens for an overall 62.5X magnification with better axial resolution than achievable through confocal microscopes. A one-channel 40x40x40um region can typically be imaged in 1 second. For super-resolution in x and z, a SIM mode is available at the expense of temporal resolution, and super-resolution may also be achieved through Super Resolution Radial Fluctuations (SRRF). The system has four lasers (405, 488, 561, and 642nm) for sequential acquisition with a quad-band bandpass filter. Samples are loaded onto 5mm glass coverslips and immersed in a 3- or 12-mL media bath between the inclined objective lenses.

Abberior Facility Line easy3D STED & Picoquant TCSPC (Whitehead): Abberior Instruments FACILITY LINE easy3D STED microscope with 4 excitation lines (405nm, 485nm, 561nm, 640nm), two pulsed STED lasers (595nm, 775nm). Includes adaptive illumination package (DyMIN, RESCue, and MINFIELD) for highest resolution and live cell super-resolution imaging at ultra-low light levels. Adaptive optics (OA) compensates for aberrations to improve STED in standard samples, and allow STED deep within tissues etc. Variable spectral detection and avalanche photodiodes (APDs) provide ultra-sensitive flexible detection. Picoquant time correlated single photon counting (TCSPC) provides additional time resolved techniques such as fluorescence lifetime imaging microscopy (FLIM) and fluorescence correlation spectroscopy (FCS). Includes steady focus during all STED modes to circumvent drift. Water, silicone, and oil lenses available to match sample refractive index for increased signal and resolution. Live cell chamber for time lapse images (utilizing adaptive illumination decreases photodamage and extends imaging speeds and durations).

Miltenyi UltraMicroscope Blaze Large fFeld of View Light Sheet (HSRB II): A fully automated light sheet microscope for imaging large or multiple cleared samples at subcellular resolution. It has a large sample chamber, holds 500mls of imaging solution, and allows for uni- and bi-directional illumination with 1-6 sheets. With 1.1X, 4x and 12x objectives one can achieve up 30x magnification and visualize large, cleared samples at subcellular resolution. This includes organoids, organs and tissue, as well as whole small animals.

Multiphoton:

Zeiss 710 NLO (Clinic B): This multiphoton allows for intravital (live animal) imaging with high magnification and resolution. This microscope is equipped with a Chameleon Vision S tunable multiphoton laser (680 nm to 1050 nm) that can penetrate farther into tissue than a traditional confocal laser. This system is mounted on an upright Zeiss Axioexaminer microscope, together with a flexible large area stage for imaging live mouse single cells, thick tissue sections, and cell lines. The confocal optics of the 710 house spectral detectors coupled with six lasers lines (405, 458, 488, 514, 543, and 633nm) for flexible acquisitions. Two non-descanned detectors (NDDs) provide ultrasensitive detection of multiphoton signals. Oil, air and water immersion objective lenses are available.

Leica SP8 (Whitehead): The Leica SP8 is an upright confocal and multiphoton microscope with a Coherent Chameleon Vision II laser tunable from 680 to 1080nm. Two highly sensitive non-descanned GaAsP based HyD detectors provide imaging of multiphoton processes. The confocal unit houses an infinitely flexible prism based spectral detector system and multiple excitation laser lines (458, 476, 488, 496, 514, 561, 594nm) for a vast variety of experimental and labeling options (coupled with LASX unmixing software for experiments with potentially 10 or more colors). Four channel detection, via two PMTs and two extremely sensitive Leica HyD detectors (GaAsP based), together with resonant scanning provides high speed imaging. A CCD camera allows– for brightfield and Dodt Gradient Contrast (DGC) for label free imaging and sample navigation. A stage and objective warmer facilitates numerous live cell imaging approaches such as FRET, FRAP, and photoconversion. A 12 kHz resonant scanner provides high speed scanning at up to 428 fps, and there is automated tiling and image stitching. Oil, air, and water immersion objective lenses are available.

Widefield fluorescence:

Zeiss Axioplan 2 (Winship): The motorized Zeiss Axioplan 2 is equipped for routine widefield epifluorescence and transmitted light applications (DIC, phase, and brightfield) using a range of high-end Zeiss Plan-Apo objectives. A Zeiss Axiocam color camera allows for histology imaging or fluorescence imaging via multiple filter sets.

Olympus IX71 (HSRB I): The inverted IX71 can perform epifluorescence and transmitted light microscopy. It contains long working distance objectives that allow for visualization through plastic culture dishes or glass. A sensitive color QImaging CCD camera and multiple filter cube sets provides fluorescence imaging in monochrome mode, and histology images in color mode.

Leica Thunder (HSRB II): The Leica Thunder wide field offers 3D live cell imaging and helps to maintain optimal physiological conditions by minimizing photobleaching, providing high performance imaging and will provide clear details in real time without out of focus blur utilizing Leica's Computational Clearing. It is a fully motorized DMi8 microscope with a highly sensitive K8 camera and a multi-line, high-intensity fluorescence LED light source and will allow for optimal physiological conditions, keeping photobleaching to a minimum while providing high performance imaging. It has a Tokia Hit stage top environmental chamber at 37° C and 5% CO₂ required for live cell imaging.

Olympus IX51 (Winship): The inverted IX51 can perform epifluorescence and transmitted light microscopy. It contains long working distance objectives that allow for visualization through plastic culture dishes or glass. An Infinity CCD monochrome camera allows for sensitive acquisitions from multiple filter set options.

BioTek Lionheart FX (Whitehead): The compact Lionheart FX widefield microscope provides flexible automated acquisitions in fluorescence, brightfield, and color imaging modes, together with multiple lenses and 37°C and 5% CO₂ control allowing live cell multiple plate reading, to IHC, and widefield-deconvolution.

Keyence BX81 (Clinic B): The Keyence BTX is a bench top epifluorescence microscope with flexible stage adaptors allowing imaging of up to 3 slides and different types of multi-well plates in both fluorescence and color imaging modes. Multiple field of views can be acquired, with a flexibility to stitch these images.

Image Analysis:

Five image analysis workstations across the five ICI locations are available, ranging from Dell workstations to custom built towers designed to handle Terabite sized data sets. Users can analyze their data using a full suite of image analysis options. These include Bitplane Imaris, Volocity 6.2, Fiji Is Just ImageJ (FIJI), and CellProfiler. Deconvolution is available via Microvolution. Custom Fiji macros and java plugins can be tailored to individual needs and are available to download. Video analysis tutorials are also publicly available on YouTube via the channel NoPhotonLeftBehind. MATLAB/Python code can be designed for stand-alone usage or for direct interface within Imaris.

Update: April 2023

FACILITIES & OTHER RESOURCES

Specific Fields Relevant for TMF Users

The Emory Mouse Transgenic and Gene Targeting Core (https://www.cores.emory.edu/tmc/) provides state-of-the-art equipment and expertise for making genetically engineered mouse models, moving alleles on or off campus, or cryopreserving existing strains of mice.

Laboratory:    The Mouse Transgenic and Gene Targeting Core Facility (TMF) is located on the ground floor of Emory Health Sciences Research Building and occupies laboratories EG41 and EG42. The EG42 space includes a fully equipped tissue culture suite dedicated to embryonic stem (ES) cell culture, embryology laboratory, microinjection/embryo manipulation space, and surgical suite.  The EG41 room includes molecular biology space, and cryopreserved embryo/sperm archival space. The animal holding/breeding room is located in EG57 is part of the animal facility and is operated by the Division of Animal Resources (DAR) as detailed below.

 In total, the core facility is fully equipped to perform all experimental procedures associated with the production of gene edited mice, (see major equipment listed below). In addition, the core facility has research space and equipment to assist laboratories with auxiliary procedures for the production and analysis of transgenic and gene targeted mice. These include rederivation and cryopreservation services, and custom mouse needs.

 Clinical:  N/A

Animal:  The animal facility is located on the ground floor of the Health Sciences Research Building (HSRB). All the mice used by the core for the production of gene edited mice are housed in this facility.  It is managed by the Emory University Division of Animal Resources (DAR) in strict compliance with the standards and policies of the Public Health Service. Mice are housed in the ventilated auto-water caging system and are changed under laminar flow hoods. The DAR staff is responsible for daily care of the animals as well as health monitoring and surveillance. The DAR also maintains vigorous quarantine and sentinel programs.

Computer:  The TMF Core facility staff has personal computer workstations that support their core activities.

Office:  The TMF has 100 sq ft of dedicated office on the 1st floor of the Health Sciences Research Building, which provides for meeting customers, and TMF team meetings. Dedicated work space for TMF staff is also located in HSRB animal facility.

Other:  N/A

Updated: April 2023

Specific Fields Relevant for TMF Users

Emory Mouse Transgenic and Gene Targeting Core (TMF): The Emory Mouse Transgenic and Gene Targeting Core provides state of the art equipment and expertise for making genetically engineered mouse models, moving alleles on or off campus, or cryopreserving existing strains of mice. With laboratories and animal facilities located on the ground floor of the Health Sciences Research Building (HSRB), the TMF provides rodent-related services that are supported by the following infrastructure.

Microinjection/Gene Editing (EG42)

Microinjection Station #1:

Leica DMi8 Inverted microscope with Phase contrast and DIC optics

Narishige manual micromanipulators

Eppendorf microinjectors

Eppendorf FemtoJet 4i transjector

Prime Tech PMM4G Piezo Impact Drive

Brook Industries heating/cooling Thermal Stage System

Microinjection Station #2:

Leica DMi8 Inverted microscope with Phase contrast and DIC optics

Narishige manual micromanipulators

Eppendorf microinjectors

Eppendorf FemtoJet 4i transjector

Brook Industries heating/cooling Thermal Stage System

Embryo collection, manipulation, and rederivation (EG42)

Leica M80 Binocular Stereo Microscope with heating stage (x2)

Leica M60 Binocular Stereo Microscope

Panasonic CO2 Incubator (x2)

Sutter P-87 Micropipette puller

BTX Electroporation system

ES Cell Culture (EG42)

Nuaire Class II Biological Safety Cabinet

ThermoScientific centrifuge

Eppendorf Centrifuge

Panasonic CO2 Incubator

Leica DMi1 Inverted Microscope

BioRad Electroporation Unit

Sperm/Embryo Cryopreservation (EG41)

FTS Systems Bio-Cool IV

Locator 4 Liquid Nitrogen Dewar

MVE Liquid Nitrogen Dewars (x9)

CEROS-2 Animal Sperm Analyzer

Molecular Biology (EG41)

Ohaus Explorer Analytical Balance

Beckman-Coulter Allegra 64R high-speed Centrifuge

ABI 9700 thermal cycler (x2)

Thermo Scientific NanoDrop Spectrophotometer            

Nuaire Class II Biological Safety Cabinet

Fisher Marathon 16KM Centrifuge

Analytik Jena VisionWorks gel imaging system

                                                                                       FACILITIES & OTHER RESOURCES

                                                                                           Updated: 30 June 2022

ROBERT P. APKARIAN INTEGRATED ELECTRON MICROSCOPY CORE (IEMC)

The Robert P. Apkarian Integrated Electron Microscopy Core (IEMC), one of the Emory Integrated Core Facilities (EICF), provides services and training on conventional transmission electron microscopy (TEM), cryo-transmission electron microscopy (Cryo-TEM), single particle cryo-electron microscopy (SP-Cryo-EM), cryo-electron tomography (Cryo-ET), conventional scanning electron microscopy (SEM), and cryo-scanning electron microscopy (Cryo-SEM). The IEMC supports academic, clinical, and industry users at two sites on Emory’s campus. Its focus and technical expertise aim to generate structural data from biological and non-biological specimens to support research in basic, biomedical, and material sciences and engineering.

The facility has recently incorporated micro-electron diffraction (micro-ED), cryo correlated light and electron microscopy (cryo-CLEM), and cryo electron microscopy of vitrified sections (CEMOVIS). Additionally, the acquisition of a Gatan K2 direct electron detector complements the existing DE20 direct electron detector for our cryo-EM and cryo-ET applications. The IEMC is supported by a qualified, supportive staff who not only contribute to research with their expertise but also with their commitment to training investigators (students, technicians and postdocs) on the various EM workflows. Users can utilize IEMC services autonomously or request IEMC staff to either assist or carry out entire workflows for them.

The Biochemistry Connector Site (ground floor of Rollins Research Center) hosts a state of the art Talos Arctica (200 kV) microscope for high-throughput acquisition of high-resolution SP-Cryo-EM data, equipped with a Gatan K3 direct electron detector and a Gatan Image Filter (GIF). For TEM and cryo-TEM sample imaging and screening, users have access to the Talos L120C (120 kV) instrument. In addition, this site includes a wet-lab space for room temperature sample preparation and a dedicated cryo-EM sample preparation area with a Gatan CP3 and a Vitrobot Mark IV plunge freezers.

The Emerson Site (ground floor of Cherry Logan Emerson Hall) includes dedicated wet-lab space for TEM preparation and processing, and immunocytochemistry. It hosts a Hitachi HT7700 (120 kV) for TEM, a JEOL JEM1400 (120 kV) for TEM, tomography of sectioned materials, and cryo-TEM, and a JEOL JEM2200FS (200kV) equipped with two direct electron detectors (Direct Electron DE20 and Gatan K2) for SP-Cryo-EM, Cryo-ET, and micro-ED. A Leica DM6 FS, with STP8000 allows acquisition of fluorescence data for cryo-CLEM. The IEMC is also equipped with Topcon SEMs for imaging and elemental analysis, as well as cryo-SEM of frozen-hydrated samples. Users also have access to a Vitrobot Mark IV to prepare cryo-EM samples, microtomes and cryo-ultramicrotomes for thick, semithin, and ultrathin microtomy, high-pressure freezing and cryo-substitution equipment for CEMOVIS or sample embedding, and sputter coaters for ultrathin metal film coating for room temperature and cryo-preserved specimens.

Together with the Emory Integrated Computational Core (EICC) and Emory’s Library & Information Technology Services, the IEMC also supports High Performance Computing with our Glacier Computation Cluster. Our staff also offers support for image analysis and processing for grants and publications.

MAJOR EQUIPMENT

Updated: 30 June 2022

Major Equipment for Robert P. Apkarian Integrated Electron Microscopy Core (IEMC) Users

ROBERT P. APKARIAN INTEGRATED ELECTRON MICROSCOPY CORE (IEMC)

The Robert P. Apkarian Integrated Electron Microscopy Core (IEMC), one of the Emory Integrated Core Facilities (EICF), provides services and training on conventional transmission electron microscopy (TEM), cryo-transmission electron microscopy (Cryo-TEM), single particle cryo-electron microscopy (SP-Cryo-EM), cryo-electron tomography (Cryo-ET), conventional scanning electron microscopy (SEM), and cryo-high resolution scanning electron microscopy (Cryo-HRSEM). The IEMC supports academic, clinical, and industry users. Its focus and technical expertise aim to generate structural data from biological and non-biological specimens to support research in basic, biomedical, and material sciences and engineering.

Emerson Site:

Three Transmission Electron Microscopes: The Emerson site houses TEMs suitable for imaging biological and non-biological specimens prepared using a number of methods both at room temperature and under cryo-conditions.

JEOL JEM-2200FS, 200 kV with in-column Omega filter and phase plates (Zernike and hole-free): This field emission TEM is set up for the semi-automated data acquisition of both single particle cryo-TEM data and tilt series for cryo-electron tomography. It is equipped with two direct electron detection devices (Direct Electron DE20 and Gatan K2) for high-resolution imaging and a Gatan US4000 CCD camera for screening.

JEOL JEM-1400 120 kV LaB₆ TEM with a Gatan US1000 CCD camera: Capable of all modes of TEM, including tomography of sectioned materials, cryo-TEM and conventional TEM. Semi-automated data acquisition is available for testing cryo-TEM grids. A Minimum Dose System (MDS), as well as the Serial EM software allow for imaging of beam-sensitive samples. A beam blocker allows for electron diffraction experiments.

Hitachi HT-7700 120 kV TEM with Tungsten filament and AMT CCD camera: Capable of all modes of TEM, including tilt imaging, electron diffraction, high contrast, and high resolution. A motorized goniometer allows +/- 70° sample tilting.

Leica DM6 FS cryo-CLEM microscope: This fixed-stage fluorescence microscope, with a closed cryo stage, is suitable for cryo-fluorescence imaging that can be correlated with transmission electron microscopy images or tilt series on our JEOL JEM2200FS using Serial EM.

Holders for Cryo-EM image acquisition: Two Gatan 626 holders for untilted data collection and 2 Gatan 914 holders for acquisition of tilt series (tilted data).

Two Scanning Electron Microscopes (SEMs): Topcon DS-130F and Topcon DS-150F Field Emission SEM/STEM with BSE (back-scattered electron detection), capable of in-lens and below-lens conventional SEM, and in-lens cryo-HRSEM. The Topcon DS-130F is fitted with an Oxford Instruments, INCAx-sight, x-ray detector to carry out Energy-Dispersive Spectroscopy (EDS) for elemental analysis. Capable of accelerating voltages from 0.5 kV - 30 kV, with Schottky field emission sources and Gatan CT-3500 cold stages.

Coating systems: For the application of metal films on support surfaces and samples.

Denton DV-602 Turbo Magnetron Sputter System with a chromium target: For metal film coating of specimens in preparation of SEM and cryo-SEM data acquisition.

Denton Benchtop Turbo Carbon/Gold Evaporator: For applying thin layers of carbon or gold on surfaces, SEM samples, or specimen support grids.

Four Ultramicrotomes: For producing semithin and ultrathin sections from embedded tissues or prepared materials at room temperature or under cryo conditions. Three ultramicrotomes for room temperature ultrathin and semithin sectioning of resin embedded samples (Leica UC6, Leica Ultracut S, and RMC Power-Tome PC). One cryo-ultramicrotome (Leica UC6i/FC6) for sectioning under cryo conditions.

BALTEC HPM 010 High Pressure Freezing Machine: For preparing frozen specimens including thick samples and monolayer cell cultures.

Leica AFS Cryo-Substitution: This instrument is designed for dehydration and fixation of cryo-preserved specimens followed by gradual temperature increase and resin embedding.

ThermoFisher Vitrobot Mark IV: For plunge freezing of aqueous solutions and cell suspensions in liquid ethane or propane for cryo-TEM or cryo-ET data acquisition.

Quorum GloQube Plasma Cleaner: To prepare support films by glow discharging for conventional and cryo electron microscopy. This instrument hosts a separate chamber for special treatment of support films with various gases.

Imaging Data Processing and Analysis: Three iMac workstations with Microsoft, Adobe, ImageJ, and IMOD software packages. Other image processing software packages installed as needed.

Biochemistry Connector Site:

Two Transmission Electron Microscopes: The IEMC – Biochemistry Connector site houses TEMs suitable for imaging biological and non-biological specimens at room temperature and under cryo-conditions.

FEI Talos Arctica (200 kV) with Bio-Quantum/K3 direct electron detector and Autoloader system: This instrument is used for cryo-grid screening and for automated, high-throughput acquisition of high-resolution, single particle cryo-EM data. It uses both ThermoFisher EPU and Serial EM for data acquisition.

FEI Talos L120C (120 kV) with LaB6 and 4k CETA detector: For negative stain and cryo-grid screening.

Holders for Cryo-EM Image Acquisition: One Gatan 626 cryo-transfer holder to be used on the FEI Talos L120C.

ThermoFisher Vitrobot Mark IV and CP3 Plunger - Gentle blot (Model 930): For plunge freezing aqueous solutions and cell suspensions in liquid ethane or propane for cryo-TEM or cryo-ET data acquisition.

Denton Benchtop Turbo Carbon Evaporator: For carbon coating of grids.

Plasma cleaning systems: To prepare support films by glow discharging for conventional and cryo electron microscopy. These systems include a Solarus Plasma Cleaning System (Model 950) for cleaning of grids and sample holders and a Pelco Easy glow for glow discharging.

Imaging Data Processing and Analysis: Glacier (Computation Cluster: 3 GPU nodes and 4 CPU nodes) with image processing software, such as Relion, CisTEM, and EMAN2/Sphire.

FACILITIES & OTHER RESOURCES

Updated: 1 September 2020

Fields Relevant for the Rodent Behavioral Core (RBC)

RODENT BEHAVIORAL CORE (RBC)

The Rodent Behavioral Core (RBC), one of the Emory Integrated Core Facilities (EICF), provides rodent behavioral analysis services. Dr. David Weinshenker is the Scientific Director and Dr. Jason Schroeder is the Core Director who runs the day to day operations and provides services for investigators. The core facility has approximately 1300 sq. ft. of space dedicated to this core within the larger Division of Animal Resources (DAR) facility in the Whitehead Biomedical Research Building. The core space includes three mouse and/or rat testing rooms, and isolated cubicles for particularly sensitive tests. At present, the following items and tests have been developed and validated by the Core and/or the Weinshenker lab:

Locomotor activity

1. Novelty-induced locomotor activity

2. Circadian rhythm

Arousal and attention

1. Behavioral sleep latency

2. Latent inhibition

Coordinated movement

1. Rotarod

2. Grid performance test

3. Automated gait analysis

4. Beam traversal

5. Pole test

6. Abnormal involuntary movements (AIMs) scoring

Learning and memory

1. Morris water maze

2. Radial arm maze

3. Y-maze

4. Social memory/discrimination test paradigm

5. Novel Object Recognition

6. Fear Conditioning

Anxiety/Stress

1. Elevated plus maze

2. Light/dark box

3. Open field

4. Social defeat

Depression

1. Forced swim test

2. Tail suspension test

3. Novelty-suppressed feeding

4. Chronic unpredictable stress

5. Sucrose consumption/preference

6. Social defeat

Seizure susceptibility

1. Flurothyl seizure chamber

2. Kanic acid seizures

3. Pentylenetetrazole seizures

4. Bicuculline seizures

5. Audiogenic seizures

6. Electrical kindling

7. Increasing current electroshock seizures

8. Pilocarpine seizures

Reward/Reinforcement

1. Drug-induced locomotor activity

2. Drug-induced stereotypy

3. Sensitization

4. Conditioned place preference

5. Oral self-administration

6. Operant drug self-administration and reinstatement

7. Operant drug discrimination

8. Operant cocaine vs. food choice

Aggression

1. Resident-intruder aggression

2. Social defeat

Sensorimotor Gating

1. Acoustic startle

2. Prepulse inhibition

General hardware/software

1. 24 rat operant self-administration chambers (Med Associates) (6 of these are equipped with laser systems for optogenetics – see next line below)

2. 6 OEM 150mW 473nm Laser systems for optogenetics

3. 4 shock generators

4. 24 SDI automated locomotor activity chambers

5. 2 SDI automated conditioned place preference chambers

6. Clever Systems automated MazeScan software

7. Video-EEG electrical seizure apparatus (two Grass S44 stimulators, two Grass SIU5 stimulus isolators, two Grass CCU1 constant current units, oscilloscope)

8. 6 rat cages equipped with running wheels

9. 8 rat cages equipped with removable wire mesh enclosure for social defeat paradigm
10. 6 video cameras

11. 1 IntelliCage system

12. 4 Coulbourn Fear Conditioning Chambers

13. 4 SDI SRI-LAB chambers

MAJOR EQUIPMENT

Updated: 1 September 2020

Major Equipment for Rodent Behavioral Core (RBC) Users

RODENT BEHAVIORAL CORE (RBC)

The Rodent Behavioral Core (RBC), one of the Emory Integrated Core Facilities (EICF), provides rodent behavioral analysis services. Major equipment includes:

1. Clever Systems automated MazeScan software (2). This tracking software is used in combination with our multiple mazes and apparatuses. It allows for digital recording and unbiased scoring of behavior. One system is used for tracking mouse behavior and the second is used for tracking rat behavior.

2. Stand-alone rodent enclosures used in combination with the Clever Systems tracking system for animal testing. We have 2 water mazes (1 for mice and 1 for rats), 2 Elevated Plus Mazes (1 for mice and 1 for rats), 2 forced swim test enclosures (1 for mice and 1 for rats), 2 mouse social investigation enclosures, 2 mouse open fields, 1 rat open field, 1 mouse light/dark box, 1 mouse zero maze, 2 rat CPP chambers, 2 mouse Novel Object Recognition enclosures, and 1 mouse Y-maze.

3. Eight Coulbourn Fear Conditioning Chambers (4 for mice and 4 for rats). These systems are equipped with cameras and software for analyzing fear behavior as evidenced by contextual or cued freezing.

4. Six OEM 150mW 473nm Laser systems for optogenetics. These systems can be used in combination with six of our operant chambers or on their own for optogenetic stimulation.

5. Twelve rat operant self-administration chambers (Med Associates) Six of the operant chambers are compatible with laser systems for optogenetics. These chambers allow for investigating a variety of operant behavior including and not limited to food and drug taking and relapse, drug discrimination, as well as responding for optogenetic manipulations.

6. Six mouse operant self-administration chambers (Med Associates). These chambers allow for investigating a variety of operant behavior including and not limited to food and drug taking and relapse, and drug discrimination.

7. 32 SDI automated locomotor activity chambers. These systems measure ambulation and general circadian activity in mice and rats.

8. 4 SDI automated conditioned place preference chambers. These chambers assess conditioned place preference/aversion.

9. 6 rat cages equipped with running wheels.

10. Six video cameras for use in combination with our tracking software or on their own.

11. One IntelliCage system. Up to ten mice can be implanted with transponders to monitor their fluid intake behavior with minimal handling. Multiple measures of operant behavior and fluid intake can be analyzed using this system.

12. Four SDI SRI-LAB chambers. Each unit measures startle behavior as well as pre-pulse inhibition, an animal model of schizophrenia-like behavior.

FACILITIES AND RESOURCES

Updated: 1 September 2020

Fields Relevant for HPLC Bioanalytical Core (HPLC) Users

HPLC BIOANALYTICAL CORE

The HPLC Bioanalytical Core (HPLC), one of the Emory Integrated Core Facilities (EICF), is supported by the Department of Pharmacology and Chemical Biology and the Emory University School of Medicine. The HPLC Bioanalytical Core measures monoamines, purines, and amino acids using HPLC methods in biological matrices including tissue extract, cell lysate, plasma, serum, CSF, urine, microdialysate. In addition, we provide expertise to develop and validate HPLC method to measure some drugs, endogenous compounds, peptides, and proteins.

The HPLC is located at the Woodruff Memorial Building Room 6306 and occupies 400 sq.ft of space. The core is equipped with three HPLC systems, which include two ESA CoulArray detection systems and one Waters HPLC system. The Core also has access to additional equipment for sample preparation including a SpectraMax M5e spectrophotometer (Molecular Devices, Sunnyvale CA) which is a UV/Vis variable wavelength microtiter plate reader with Softmax Pro software used for performing colorimetric spectrophotometrical protein assays, and Branson sonifier 450 which is used for tissue homogenization. Also available are a Millipore Water system, centrifuges, sonicator, pH meters, balances, oven, refrigerators, hot plates, stirrers, -70C freezers, and other standard equipment.

MAJOR EQUIPMENT

Updated: 13 June 2022

Major Equipment for HPLC Bioanalytical Core (HPLC) Users

HPLC BIOANALYTICAL CORE (HPLC)

The Rollins School of Public Health (RSPH) HPC cluster is a system that consists of 25 compute nodes, 24 of which have 32 compute cores and 192GB of RAM each. The last node is a “large memory node” with 1.5 TB of RAM. These systems are connected together via 25GB Ethernet network, and all have access to a shared 1 Petabyte Panasas parallel file system.

In addition to the hardware, the system runs the CentOS Linux operating system (currently version 8), which is a “white-box” implementation of the Red Hat Enterprise Linux OS that purports to be 100% binary compatible with the commercial version.

Job scheduling is handled by the SLURM job scheduler, which is an application that currently runs on the majority of the Top 500 supercomputing sites in the world.

RSPH Server Services:

Virtual Server Services: RSPH server platforms are provided by both standalone systems and virtual servers through a VMware system. The RSPH VM platforms provide over 100 virtual servers that are used for administrative, teaching, database, and research needs. RSPH IT deploys both Windows and UNIX environments. Cloud server services are growing as part of the infrastructure as well, spanning SAAS, PAAS, and IAAS systems hybridized back to the campus and local systems. These servers are divided to be open or highly secure to comply with HIPAA and FISMA Moderate-defined controls. Some specific physical server platforms are deployed for performance and compatibility requirements for some application systems.  An example is our database platform.

Internet/Web Services: RSPH uses a central IT services resource, Microsoft Office365, for our email and is a secured, sensitive data system. RSPH uses the Cascade content management system to update and generate content for our main school website.  All Rollins web content is served up through local RSPH web servers, which also support center, program, administrative, and personal faculty research websites.  RSPH IT offers a number of application environments to support administrative and research endeavors such as Cold Fusion development and support for JAVA-based applications. RSPH has an intranet system that focuses on providing online information and access to the various services at RSPH. This is done through a dedicated platform using the product Noodle.

Data Storage: Data storage is provided across a number of layers and services that use local network accessed systems, central IT network storage systems, and cloud-based storage. We provide over a petabyte of central IT storage for research needs and back-up services. Additional on-demand storage for research or server systems support can be acquired through central IT. All storage services are HIPAA secure. Collaborative storage areas for file sharing are provided through products like Box and OneDrive. These storage areas are HIPAA secure and can be set up for external collaborations.

Database Services: RSPH IT provides primary secure database services utilizing Microsoft SQL Server. These databases are used for application systems across our administrative and research needs. Database accounts are available to faculty members upon request.

Network Environments:

The RSPH network is connected to the Emory Campus backbone via a 10 Gigabit Ethernet connection, making campus services and wide area network services readily available.  RSPH also has an extensive wireless network providing “N” class connections and speeds that cover all of the school’s buildings and nearby external areas.  This network offers guest services as well as secure services for students, faculty and staff.  All of the secured services inside the school’s firewalls—including network storage and other services—can be access through the Emory VPN using two-factor authentication. Integrated printing, faxing, and scanning services are provided throughout RSPH buildings and are integrated with our network storage systems.

Applications, Informatics, and Application Development Systems:

Over 40 applications, statistical platforms (SAS, R, STATA, SPSS), and various programming and research analytics (quantitative and qualitative) applications are provided to integrate full lifecycle research informatics needs.  Examples of these are survey instruments such as Redcap and Qualtrics and various form-based data entry systems. Laboratory informatics support is available through a Thermo Laboratory Information Management system and specimen tracking system, Open Specimen. Integration with external mail and CRM systems such as Mailchimp and Salesforce are provided. Cloud-based services for potential student interaction are provided through systems such as Slate.  HIPAA secured data visualization and dimensional manipulation platforms include Tableau, PowerBI, and Business Objects. GIS application platforms such as ARCGIS are supplied on an enterprise license. Application development platforms provided include: Rstudio, Cold Fusion, database management tools, and others. Many of these general application systems are centrally funded through RSPH IT and supported. Specific applications that a researcher may need are supported and installed upon request. The Central IT Research IT group provides a number of tools such as the data warehouse I2B2 which lets you query Emory Healthcare electronic health record data for patient counts and aggregate information.

End-Node Computing:

Desktop Computing: RSPH provides a set of standard laptop and desktop systems to choose from for our faculty and staff. Recommendations for standard computing configurations for student computing success is provided. The higher-end analytic systems have at least a I7 CPU configuration with a minimum of 16GB of RAM memory, 21 inches or higher flat panel monitors standard with 500 gigs local disk space, and 64-bit Windows. RSPH’s Apple environments are generally iMac configurations or MacBook laptops with at least 16 gigs of memory. In many cases, multiple monitors are deployed well. A number of our researchers have expanded the computational desktop resources for their systems to drive high performance computation with extensive memory, specialty CPU/GPUs, and extended local storage.

Many RSPH staff and faculty have multiple systems that include docking laptops and other mobile devices such as tablets. All of our desktop and laptop systems are connected to our network storage that provides both highly secure and access controlled, sharable folders. RSPH provides support for all types of mobile devices such as tablets and smartphones. These mobile devices are often used in RSPH research as field data collection devices.

Virtual Desktop Computing: We have incorporated Apporto's cloud-based platform into our Emory RSPH virtual desktop. This platform provides access to over 40 applications needed while learning at Rollins. No installation or download of software is required—which means more hard drive space for your computer. Simply open a browser and use any available application through the virtual environment.

Information Security:

RSPH’s IT environment is a HIPAA-covered entity and complies with HIPAA and Emory information security and privacy policies and practices. In compliance with these policies and practices, RSPH aligns with the National Institute of Standards and Technology special publications (800 series) for identifying, assessing, and managing information security risk within a technology environment. Drawing on federal and industry best practices, RSPH has implemented a series of multi-layered security controls to protect the integrity, reliability, and confidentiality of data. All systems that access our infrastructure are scanned for vulnerabilities and any identified vulnerabilities are assessed and managed. Security policies are created and reviewed through the Woodruff Health Sciences Center HIPAA committee, the Emory University Technology Infrastructure and Policy committee, and local policies through the Rollins Information Technology Advisory committee.

Facilities & Other Resources

Updated: 1 June 2022

TRANSLATIONAL NEUROSCIENCE CORE (TNC)

The Translational Neuroscience Core (TNC), one of the Emory Integrated Core Facilities (EICF), is supported by the Department of Neurosurgery and the Emory University School of Medicine. The TNC supports investigators interested in translation of new therapies at an accelerated pace, providing the necessary tools for clinical translation. In addition to specialized neurosurgical services, the TNC also provides investigators and customers with consulting services in the field, as well as preparation of Animal Protocols and Final Reports. The TNC performs its surgical activities at Emory’s Division of Animal Resources (DAR) or at Yerkes National Primate Research Center. The TNC surgeons also perform its surgical activities at Contract Research Organizations – CROs, at the discretion of its customers. Individual members of the Translational Neuroscience Core have personal workstations to support their core activities and share office / laboratory space on the 6th floor of the Woodruff Memorial Research Building. The Translational Neuroscience Core is available for users in the Georgia Core Facilities Partnership (Emory, Yerkes, GA Tech, Morehouse, GSU, UGA, Mercer University, Morehouse School of Medicine, Clark Atlanta, Augusta University), as well as external users from industry.

MAJOR EQUIPMENT

Updated: 1 June 2022

Specific Fields Relevant for Translational Neuroscience Core (TNC) Users

TRANSLATIONAL NEUROSCIENCE CORE (TNC)

The Translational Neuroscience Core (TNC), one of the Emory Integrated Core Facilities (EICF), is supported by the Department of Neurosurgery and the Emory University School of Medicne. The TNC is located on the 6th floor of the Woodruff Memorial Research Building. The TNC laboratory area includes dedicated office space for administration and management of its resources. It also includes adjacent storage space for its equipment. For procedures performed at Emory University, Emory Division of Animal Resources - DAR - provides facilities, personnel and equipment for animal care.

TNC equipment includes:

OmniPlus/OSM200 Surgical Microscope: Microscope includes integrated 4K Streaming video and 19" Exor Vision LCD Monitor.

Midas Rex™ Legend Stylus® High-Speed Neurosurgical Drill

Sterrad NX Sterilization System: A next-generation low-temperature hydrogen peroxide gas plasma system that offers fast terminal sterilization with a standard 28-minute cycle time and an advanced 38-minute cycle time.  The system can sterilize a wide range of instruments, including single-channel flexible endoscopes, semi-rigid ureteroscopes, power drills, batteries, cameras, light cords, rigid scopes, general surgical instruments, and more. The system provides the flexibility of having dry, packaged, sterile instruments ready when needed.

State-of-the-art Neurosurgical Equipment and Instruments for Spinal Cord Procedures

·         4 complete sets of neurosurgical tools specific for performing laminectomies

·         4 complete sets of spinal platforms designed for spinal cord injections

·         3 microinjector pumps for therapeutics delivery

·         4 external spinal immobilization apparatus

·         Customized injection cannulas for therapeutics delivery

Specialized Neurosurgical Equipment for Brain Procedures

·         Stealth hardware equipment

·         Head frames

·         Manthis catheters and pumps

·         Customized injection cannulas

State-of-the-art Neurosurgical Instruments for Nerve Repair Procedures

MAJOR EQUIPMENT

Updated: 1 September 2020

Major Equipment for Biostatistics and Collaboration Core (BCC) Users

BIOSTATISTICS AND COLLABORATION CORE (BCC)

RSPH High Performance Computing Services (HPC):

RSPH HPC Cluster Systems: RSPH is host to a Beowulf-style HPC cluster. In total, this cluster has 664 cores (providing over 1,300 threads) with over 4TB of aggregated system memory. Users of the cluster access Emory Isilon high-speed storage partitions over direct-connected fiber links. The cluster runs on 64-bit Red Hat Enterprise Linux and utilizes the Grid Engine distributed resource manager for allocating runtime and memory consumption on the system. Licensed software such as SAS and MATLAB are installed for general use on the cluster, as well as a large number of open-source software packages and programming environments, including R, Python, Fortran, and C/C++. Environment autonomy for specific and reproducible execution on nodes is supported through Anaconda. Shared code interaction is supported through Jupiter Notebook.

RSPH Server Services:

Virtual Server Services: RSPH server platforms are provided by both standalone systems and virtual servers through a VMware system. The RSPH VM platforms provide over 100 virtual servers that are used for administrative, teaching, database, and research needs. RSPH IT deploys both Windows and UNIX environments. Cloud server services are growing as part of the infrastructure as well, spanning SAAS, PAAS, and IAAS systems hybridized back to the campus and local systems. These servers are divided to be open or highly secure to comply with HIPAA and FISMA Moderate-defined controls. Some specific physical server platforms are deployed for performance and compatibility requirements for some application systems.  An example is our database platform.

Internet/Web Services: RSPH uses a central IT services resource, Microsoft Office365, for our email and is a secured, sensitive data system. RSPH uses the Cascade content management system to update and generate content for our main school website.  All Rollins web content is served up through local RSPH web servers, which also support center, program, administrative, and personal faculty research websites.  RSPH IT offers a number of application environments to support administrative and research endeavors such as Cold Fusion development and support for JAVA-based applications. RSPH has an intranet system that focuses on providing online information and access to the various services at RSPH. This is done through a dedicated platform using the product Noodle.

Data Storage: Data storage is provided across a number of layers and services that use local network accessed systems, central IT network storage systems, and cloud-based storage. We provide over a petabyte of central IT storage for research needs and back-up services. Additional on-demand storage for research or server systems support can be acquired through central IT. All storage services are HIPAA secure. Collaborative storage areas for file sharing are provided through products like Box and OneDrive. These storage areas are HIPAA secure and can be set up for external collaborations.

Database Services: RSPH IT provides primary secure database services utilizing Microsoft SQL Server. These databases are used for application systems across our administrative and research needs. Database accounts are available to faculty members upon request.

Network Environments:

RSPH Network: The RSPH network is connected to the Emory Campus backbone via a 10 Gigabit Ethernet connection, making campus services and wide area network services readily available.  RSPH also has an extensive wireless network providing “N” class connections and speeds that cover all of the school’s buildings and nearby external areas.  This network offers guest services as well as secure services for students, faculty and staff.  All of the secured services inside the school’s firewalls—including network storage and other services—can be access through the Emory VPN using two-factor authentication. Integrated printing, faxing, and scanning services are provided throughout RSPH buildings and are integrated with our network storage systems.

Applications, Informatics, and Application Development Systems:

Over 40 applications, statistical platforms (SAS, R, STATA, SPSS), and various programming and research analytics (quantitative and qualitative) applications are provided to integrate full lifecycle research informatics needs.  Examples of these are survey instruments such as Redcap and Qualtrics and various form-based data entry systems. Laboratory informatics support is available through a Thermo Laboratory Information Management system and specimen tracking system, Open Specimen. Integration with external mail and CRM systems such as Mailchimp and Salesforce are provided. Cloud-based services for potential student interaction are provided through systems such as Slate.  HIPAA secured data visualization and dimensional manipulation platforms include Tableau, PowerBI, and Business Objects. GIS application platforms such as ARCGIS are supplied on an enterprise license. Application development platforms provided include: Rstudio, Cold Fusion, database management tools, and others. Many of these general application systems are centrally funded through RSPH IT and supported. Specific applications that a researcher may need are supported and installed upon request. The Central IT Research IT group provides a number of tools such as the data warehouse I2B2 which lets you query Emory Healthcare electronic health record data for patient counts and aggregate information.

End-Node Computing:

Desktop Computing: RSPH provides a set of standard laptop and desktop systems to choose from for our faculty and staff. Recommendations for standard computing configurations for student computing success is provided. The higher-end analytic systems have at least a I7 CPU configuration with a minimum of 16GB of RAM memory, 21 inches or higher flat panel monitors standard with 500 gigs local disk space, and 64 bit Windows. RSPH’s Apple environments are generally iMac configurations or MacBook laptops with at least 16 gigs of memory. In many cases, multiple monitors are deployed well. A number of our researchers have expanded the computational desktop resources for their systems to drive high performance computation with extensive memory, specialty CPU/GPUs, and extended local storage.

Many RSPH staff and faculty have multiple systems that include docking laptops and other mobile devices such as tablets. All of our desktop and laptop systems are connected to our network storage that provides both highly secure and access controlled, sharable folders. RSPH provides support for all types of mobile devices such as tablets and smartphones. These mobile devices are often used in RSPH research as field data collection devices.

Virtual Desktop Computing: Our virtual computing environments for students, staff, and faculty are provided through our RSPH Citrix environment. This virtual desktop environment provides more than 40 applications and is accessible from any place one can get on a network and open a browser. The Citrix environment is also set up to be a highly secure environment where data does not leave the Emory systems. These virtual desktops are integrated into all the other services such as the shared storage systems. The current platform is designed to extend the on-premise capacity through virtual desktop provisions on cloud services such as AWS.

Student Kiosk Computing: Students have access to 62 additional computers in an open lab area so they can get to their email, the RSPHCitrix system, Microsoft Office products, and other campus computing resources. These computers and the lab computers are all connected to a student printing system that they can use for printing their documents. The printers are business hubs providing scanning, copying, and printing and are located across various floors and in both buildings and through the wireless network.

Information Security:

RSPH’s IT environment is a HIPAA-covered entity and complies with HIPAA and Emory information security and privacy policies and practices. In compliance with these policies and practices, RSPH aligns with the National Institute of Standards and Technology special publications (800 series) for identifying, assessing, and managing information security risk within a technology environment. Drawing on federal and industry best practices, RSPH has implemented a series of multi-layered security controls to protect the integrity, reliability, and confidentiality of data. All systems that access our infrastructure are scanned for vulnerabilities and any identified vulnerabilities are assessed and managed. Security policies are created and reviewed through the Woodruff Health Sciences Center HIPAA committee, the Emory University Technology Infrastructure and Policy committee, and local policies through the Rollins Information Technology Advisory committee.

Investigational Clinical Microbiology Core:  The ICMC supports banking and characterization of clinical isolates, environmental samples, and microbiome samples.  The ICMC has the capacity to perform detailed classification of antibiotic resistant clinical isolates such as but not limited to, sophisticated susceptibility testing procedures not routinely available in clinical laboratories, studies of synergies between combinations of antibiotics, techniques to identify heteroresistance (looking for subpopulations with resistance), molecular fingerprinting, qPCR, and genomic sequencing and analysis. 

Investigational Clinical Microbiology Core Biorepository: The ICMC biorepository contains a large collection of bacterial samples isolated by the Emory University Hospital (EUH) mircobiology laboratory as part of standard patient care, envrionmental samples and microbiome samples. These normally discarded clinical samples and specimens are processed and stored in the ICMC biorepository and made avaialbe to investigators for the purpose of subsequent evaluation, mechanistic studies, clincial correlation or novel assay development.  A corresponding database of all phenotypic laboratory characteristics of each isolate and important patient medical data is avaialbe. As of January 2022, there are over 17,000 bacterial isolates from approximately 9500 unique patients. The majority of these isolates are from blood infections.

Facilities and Resources

Updated: 06 June 2022

Investigational Clinical Microbiology Core  - Facilities and Resources 

Facilities and Resources

Fields Relevant for the Investigational Clinical Microbiology Core (ICMC)

Other

The Investigational Clinical Microbiology Core (ICMC), one of the Emory Integrated Core Facilities (EICF), was set up for banking and characterization of antibiotic resistant clinical isolates, environmental samples, and microbiome samples to support the Emory Antibiotic Resistance Center (ARC) collaborative research program. The ICMC has the capacity to perform detailed classification of antibiotic resistant clinical isolates such as but not limited to, sophisticated susceptibility testing procedures not routinely available in clinical laboratories, studies of synergies between combinations of antibiotics, techniques to identify heteroresistance (looking for subpopulations with resistance), molecular fingerprinting, qPCR, and genomic sequencing and analysis. The ICMC assists investigators with collection and obtaining clinical specimens and isolates through the ICMC biorepository.

Investigational Clinical Microbiology Core Biorepository: The ICMC biorepository contains a large collection of bacterial samples isolated by the Emory University Hospital (EUH) microbiology laboratory as part of standard patient care, environmental samples and microbiome samples. These normally discarded clinical samples and specimens are processed and stored in the ICMC biorepository and made available to investigators for the purpose of subsequent evaluation, mechanistic studies, clinical correlation or novel assay development. A corresponding database of all phenotypic laboratory characteristics of each isolate and important patient medical data is available. Currently there are over 17000 bacterial isolates from approximately 9500 unique patients. The majority of these isolates are from blood infections.

The ICMC located in a laboratory located on the 1st floor of the Health Sciences Research Building I, with approximately 400 square feet of dedicated wet-lab space and two procedure rooms that rooms include biosafety cabinets, one CO2 incubator and two non-,CO2 shaking incubators. The ICMC has a state-of-the-art BioMerieux eMag® and a ThermoFisher’s KingFisher Apex for automated nucleic acid extraction system from various sample types, a BioSwiss PetriSwiss PS200 carrousel and Proficlave PC10 media prep for rapid automated petri dish preparation. In addition to larger items of equipment listed separately, the lab contains small equipment necessary for molecular genetics and microbiology experiments (microcentrifuges, thermocyclers etc.). Typical workflows in the lab include banking and characterization of clinical bacterial isolates; growth of bacterial culture and DNA extraction; PCR, and preparation of MiSeq sequenicng libraries. The lab uses a Zebra 110 barcode printer for sample labeling and OpenSpecimen Laboratory Information Management System (LIMS). The lab uses the BioNumerics software platform for integrated analysis of all major applications in Bioinformatics: 1D electrophoresis gels, phenotype characters, and sequences. BioNumerics allows the lab to combine information from various genomic and phenotypic sources into one global database and conduct conclusive analyses. Technicians have custom-designed space for workstations in the lab and cubical office space. Dr Satola has a 100 sq ft office next door to the lab with a printer, scanner and a Dell computer with 16 GB RAM and Intel®, Core™ i7-490 CPU @3.6oGHz. All research assistants have similar computers and the lab has a designated laptop for the LIMS. Network acces is avialbe to the Emory Computer network. Dr. Satola and Dr. Babiker have access to the EUH’s Clinical Data Warehouse and Cerner Millennium (EUH electronic medical records) and Dr. Read (Co-I for ICMC) has three Linux compute clusters dedicated to analysis of genome data from his research projects. The servers are housed in the first floor of the HSRB.

The ICMC located in a laboratory located on the 1st floor of the Health Sciences Research Building I, with approximately 200 square feet of dedicated wet-lab space and two procedure rooms that rooms include biosafety cabinets, one CO2 incubator and two non-,CO2 shaking incubators. The ICMC has a state-of-the-art BioMerieux eMag® automated nucleic acid extraction system from various sample types. In addition to larger items of equipment listed separately, the lab contains small equipment necessary for molecular genetics and microbiology experiments (microcentrifuges, thermocyclers etc.). Typical workflows in the lab include banking and characterization of clinical bacterial isolates; growth of bacterial culture and DNA extraction; PCR, and preparation of MiSeq sequenicng libraries. The lab uses a Zebra 110 barcode printer for sample labeling and Nautilus Laboratory Information Management System (LIMS). The lab uses the BioNumerics software platform for integrated analysis of all major applications in Bioinformatics: 1D electrophoresis gels, phenotype characters, and sequences. BioNumerics allows the lab to combine information from various genomic and phenotypic sources into one global database and conduct conclusive analyses. Technicians have custom-designed space for workstations in the lab and cubical office space. Dr Satola has a 100 sq ft office next door to the lab with a printer, scanner and a Dell computer with 16 GB RAM and Intel®, Core™ i7-490 CPU @3.6oGHz. All research assistants have similar computers and the lab has a designated laptop for the LIMS. Network acces is avialbe to the Emory Computer network. Dr. Satola has access to the EUH’s Clinical Data Warehouse and Cerner Millennium (EUH electronic medical records) and Dr. Read (Co-I for ICMC) has three Linux compute clusters dedicated to analysis of genome data from his research projects. The servers are housed in the first floor of the HSRB.

The Medical Imaging, Informatics, and AI Core supports Emory investigators and the wider Georgia research community through the Georgia CTSA by obtaining access, curating data, analyzing data, and creating novel informatics and AI/ML solutions for single or multi-center studies. The Core consists of a team of engineers, data scientists and clinicians working together to provide expertise through an array of services including but not limited to informatics architecture design, the processing of data, real time data flows, grant generation, machine learning model development, and more. Each of the services may be tailored to fit the individual needs of each investigator.

Emory Integrated BIOREPOSITORY Core (EIBC)

Updated: April 2023

The Emory Integrated Biorepository Core (EIBC) will provide research support to investigators by preserving high-quality fully automated Hamilton BiOS -80 ^oC biorepository storage of their research samples.

Initially, investigators in HSRB I and HSRB II will have the priority for its utilization.  This instrument is not intended to be a solution to Emory’s overall biobanking challenges, its purpose is to provide an alternative to a significant number of -80 freezers in the HSRB II building, maximizing the amount of wet laboratory space through the building.  The Hamilton BIOS M7 unit has been configured to hold over 3 million samples using the Hamilton selected tube size of 0.6mL and 2.0mL using high density rack ware.

The Emory Integrated Biorepository Core (EIBC) is subsidized by the Emory University School of Medicine and is one of the members of Emory Integrated Core Facilities.

FACILITIES & OTHER RESOURCES

Updated: April 2023

Fields Relevant for the Emory Integrated Biorepository Core (EIBC)

The Emory Integrated Biorepository Core (EIBC), one of the Emory Integrated Core Facilities (EICF), consists of a fully automated Hamilton BiOS M7 -80 ^oC biorepository freezer which provide unique services to Emory clinical and basic researchers. The Hamilton BIOS M7 unit has been configured to hold over 3 million samples using the Hamilton selected tube size of 0.6mL and 2.0mL using high density rack ware.

The central mission of the EIGC is Mission and Goals: The Emory Integrated Biorepository Core (EIBC) is built with the strong commitment to provide short- and long-term open collaborative support to all School of Medicine Faculty at Emory University with a primary goal to provide storage, tracking, and retrieval of biospecimens necessary for their research goals.

The EIBC staff: The core Director is Dr. Mohammad S. Hossain, a PhD-scientist with extensive biorepository related experience. Dr. Hossain is responsible for handling the day-to-day functioning of the EIBC by using the OpenSpecimen-Hamilton BiOS softwares bi-directional LIMS set up the Sharon Mason team of Emory OIT. Scientific Director, Carlos S. Moreno, PhD (Associate Professor Department of Pathology & Laboratory Medicine) provides overall project planning and grant application support as needed. One full-time tech is in the hiring process to support the routine EIBC work along with Dr. Hossain. The EIBC team works closely with Wayne A. C. Harris, Data Manager, Emory All of Us Research Program Informatics Analyst, the Emory Integrated Computational Core (EICC) to set up EIBC PPMS.

EIBC Location: The Emory Integrated Biorepository Core (EIBC) is located in the G2 level Room# G225 of Health Sciences Research Building II (HSRB II). HSRB-II is a trailblazing space designed to incite better collaborations and bigger impacts in biomedical research. Multidisciplinary to its core, it brings together experimental researchers, computational scientists, and core technologies to solve the biggest human health problems of our time. HSRB II brings together 1,200 biomedical researchers from cardiology, vaccinology, neurology, oncology and pediatrics and places them in a 350,000-sq.-ft. building designed to spur collaboration and innovation.

Other EIBC related information:

§  Space in the biorepository will be provided on a first come, first served basis.

§  There will be no restriction on how often one can access their materials. Access can be carried out remotely via a computer. Individuals can then pick up samples.

§  The pricing structure is currently under development.

§  Mechanical systems will be maintained under a service contract to Hamilton. 

§  The sample repository is engineered by Hamilton to provide multiple backups in the case of equipment failure. These failsafe mechanisms will ensure that samples remain at temperature in the event repairs are needed to the system.

§  EIBC is working with the SOM MII_AI Core to integrate biorepository management system with the Clinical Data Warehouse to support deep phenotyping and bioinformatics analysis.

MAJOR EQUIPMENT 

Updated: April 2023

Fields Relevant for the Emory Integrated Biorepository Core (EIBC)

Major Equipment:

·         Hamilton Biorepository (BiOS) M7 Freezer System

·         State-of-the-art automated, ultra-low temperature (-80^o C) freezer system

·         Equipped to accommodate over 3 million biospecimens.

·         Liquid nitrogen dewars adjacent to the main Hamilton biorepository.