The Electron Microscopy Research Facility (EMRF) at the UNMC Department of Pathology, Microbiology and Immunology provides advanced imaging support and technical expertise for investigators utilizing Transmission Electron Microscopy (TEM) and Scanning Electron Microscopy (SEM). The core offers specialized specimen preparation, ultramicrotomy, negative staining, and electron microscopy services to support a broad range of biological and materials research applications.

Led by Medical Director Dinesh Pradhan, MD, the facility serves University of Nebraska investigators, external academic collaborators, and industry partners, with consultation and technical support provided by experienced electron microscopy staff throughout all stages of the research.

The UNMC Tissue Sciences Facility (TSF) provides comprehensive histology, immunohistochemistry, imaging, and pathology support services for animal and human tissue research. The facility offers standardized and specialized services including tissue processing, embedding, sectioning, paraffin and frozen staining, multiplex immunohistochemistry/immunofluorescence, digital slide scanning, tissue microarray construction, and technical support for client-use instrumentation.

TSF supports investigators through expert technical guidance, pathology consultation, and training on specialized histology procedures and equipment. Services are available to University of Nebraska researchers, external academic institutions, and industry partners.

Led by Medical Director Dinesh Pradhan, MD, TSF provides expert guidance in specialized sample preparation, histology, imaging, staining, immunohistochemistry, and frozen sectioning. Skilled technologists are also available to assist researchers throughout the tissue processing and imaging workflow.

The UNMC Spatial Profiling Hub Core Facility (SPH) offers spatial omics processing on many different tissue types.  The SPH currently offers Bruker‘s GeoMx DSP, 10x Visium including HD and 3‘, G4X Spatial Sequencing Sample Prep, and Miltenyi MacSima full services. The SPH staff offers expert collaboration from project design to data handoff. The core has established workflows with additional shared resources on the UNMC campus to allow for expertise throughout your entire project.

The Multiphoton Intravital & Tissue Imaging (MITI) Core Facility, is part of the Translational Imaging and Behavioral Assessment (TIBA) Core within the Cognitive Neuroscience of Development & Aging (CoNDA) Center and larger Fred & Pamela Buffett Cancer Center Preclinical Imaging Center. The MITI Core is equipped with experienced research professionals and state-of-the-art intravital imaging equipment to acquire advanced descriptive and quantitative data for various in-vivo/preclinical imaging studies.

The MITI Core is equipped with an Olympus FVMPE-RS advanced multiphoton microscope, a multichannel, multiphoton excitation system specifically tailored for intravital and deep tissue imaging. It delivers high speed (up to millisecond imaging) for rapid in vivo imaging of physiological responses, near infrared excitation for deep tissue imaging. The Olympus FVMP-RS system is additionally equipped with 458 and 588 nm stimulation laser lines for photobleaching, light stimulation and/or photoactivation of various fluorescent or caged constructs.

The Olympus FVMPE-RS Multiphoton Microscope uses a Spectra-Physics InSight X3 dual-line, tunable multiphoton laser for ultrafast, multichannel imaging. The main output from the InSight laser is a tunable line ranging from 680 to 1300 nm with a second multiphoton excitation line at 1045 nm. This extended excitation range supports both traditional fluorophores and fluorescent proteins (blue to long range red), as well as second and third harmonic imaging.

The available Neurotar Mobile Home Cage (Funding: P20 GM130447) allows researchers to integrate real-time imaging with behavioral/locomotion tracking.

Training and access to the imaging system, support in the design of experimental procedures, acquisition of image data, and analysis of acquired images are offered through the MITI Core. Services are available to investigators within the University of Nebraska network, as well as academic or commercial/industrial institutions in the region at hourly usage rates.

The Cognitive Neuroscience of Development and Aging (CoNDA) Center is a NIH Center of Biomedical Research Excellence (COBRE) at the University of Nebraska Medical Center in Omaha, Nebraska, with a focus on neuroscience research across the lifespan. The center aims to advance translational and human neuroscience through support of research projects and development of infrastructure.

Core provides equipment, personnel, and protocols for routine and advanced cellular and molecular assays for research.

The Advanced Microscopy Core Facility (AMCF) at UNMC houses state-of-the-art imaging technologies ranging from super-resolution (~ 0.120 um to 0.020 um) to microscopic (~ 0.300 um) to mesoscopic (~ 1 um) biomedical imaging. Imaging specialists provide training and/or actively assist researchers collecting images across the diverse array of imaging instrumentation available in the AMCF with competitively priced usage fees for internal and external facility users.

The Zeiss ELYRA PS.1 is an inverted microscope for super-resolution (SR) structured illumination microscopy (SIM) and single-molecule localization microscopy (SMLM) including, PhotoActivated Localization Microscopy (PALM) using photo-switchable/convertible fluorescent proteins, Total Internal Reflection Fluorescence (TIRF) and STochastic Optical Reconstruction Microscopy (STORM).

The Zeiss 800 CLSM with Airyscan (Funding: NIH P30 GM106397) is an inverted microscope dramatically increasing conventional confocal image resolution to ~180 nm using Airyscan technology.

The Zeiss 710 LSM (Funding: NIH S10 RR027301) is an inverted microscope supporting most basic imaging applications, multi-channel and spectral, co-localization, live cell, 3D, and time series imaging.

The Zeiss Celldiscoverer 7 (Funding: NIH P30 GM106397) is a widefield imaging system for automated, time-lapse imaging of live samples.

The Zeiss Axioscan 7 (Funding: NIH P20 GM103427) is a high-performance whole slide scanning system for fluorescence and brightfield imaging.

The Miltenyi Biotec Ultramicroscope II Light Sheet fluorescence microscope (Funding: NIH S10 OD030486) extends fluorescent imaging into true 3D, large-scale volumetric imaging of intact tissues, organs, and small organisms.

The AMCF also houses several high-end data analysis workstations with premier image analysis software including HALO (Funding: NIH P20 GM103427) and IMARIS (Funding: NIH S10 OD030486) facilitating data rendering, analyses, and presentation options.

UNMC‘s Core for Advanced Magnetic Resonance Imaging (CAMRI) provides state-of-the-art research MRI capabilities for investigators at UNMC and across the greater Omaha area. Housed in UNMC’s Hixson-Lied Center, CAMRI operates a Siemens 3T Prisma MRI instrument that can collect high quality data of any MR modality using advanced gradients and research-grade pulse sequences. A variety of head coils (20-, 32-, and 64-channel) are available to optimize data collection for the needs of specific studies. Studies incorporating functional MRI can take advantage of CAMRI’s suite of MRI-compatible response devices, mirrored 32-inch LCD screen, and integrated stimulus-display computer.

UNMC\'s CAMRI receives support from the UNMC Cognitive Neuroscience of Development and Aging Center (CoNDA Center, P20GM130447), an NIGMS Center of Biomedical Research Excellence (CoBRE).

The facility provides service and expert advice to researches in their projects related to nanoimaging studies of molecular systems at single molecule and single cell levels utilizing Atomic Force Microscope, combination of Atomic Force Microscope with Fluorescence Optical Microscope, combination of Atomic Force Microscope with Raman Spectroscopy.

The Biosafety Level 3 (BSL-3) Core Facility provides a safe and secure work area for qualified and authorized researchers to perform studies that involve BSL-3 organisms.

The negative air pressure handling system, secure entrance and exit doors, five individual and secure Principal Investigator (PI)-assigned working suites, two pass-through autoclaves, annually certified biosafety cabinets, and personal protective equipment (PPE) contribute to the biosafety of each researcher using this facility.

The Bioinformatics and Systems Biology Core (BSBC) is a university-wide resource that fosters research and teaching activities related to bioinformatics and systems biology at UNMC. The mission of BSBC is to provide infrastructure, resources, and educational training in the rapidly expanding field of bioinformatics with the ultimate goal of promoting synergistic research activities at the intersection of computational and experimental disciplines. This facility will be accessible to all UNMC and outside researchers who want to analyze biomolecular datasets (DNA, RNA, proteins, etc.).

Preclinical ultrasound imaging. Vevo 3100, Vevo 3100 LAZR-X, Perkin Elmer Vega

The mission of Mass Spectrometry and Proteomics Core Facility (MSPCF) at the University of Nebraska Medical Center is to enhance the capacity for research. Our main goals are:

1. to establish an integrated proteomics program to support researchers at the UNMC in their efforts to seek extramural funding,
2. to provide high quality services,
to facilitate collaborative scientific effort with other institutions of higher education within State of Nebraska, and
3. to provide state-of-the-art environment for education of researchers in techniques of mass spectrometry and proteomics.

The UNMC Genomics Core Facility is a comprehensively equipped facility that provides genomic services on a fee-for-use basis to the greater academic research community. The core provides both Next Generation DNA and Sanger sequencing services; single cell genomics assays by 10x Genomics, and Nanostring technology targeted gene expression assays. The UNMC Genomics Core currently supports the research of over 140 independent laboratories annually. These researchers are involved in a wide variety of scientific projects of both biomedical and basic science relevance.

A small animal image guided irradiator with CT and portal imaging capabilities. An X-ray tube is attached to a gantry allowing for single beam or arc delivery of radiation to small rodent. Several collimators of varying size and shape allows for precise radiation and beam shaping to target organs or tumors. This instrument mimics the clinical setting of radiation therapy for cancer patients.

Our facility houses a state –of the art a 306-channel whole-head MEG system (TRIUX, Neo, MEGin) and 128 channels -EEG amplifier.MEG helmet does coverage for whole cortex, 1220 cm2. MEG system has three measurement positions:supine, lower and upper seated. MEG sensors are divided into two types: 102 identical plug-in triple sensors units with two orthogonal planner gradiometers flux transformers, one magnetometer flux transformer and three dc-SQUIDs (Super-conducting QuantumInterference Devices). Size of gradiometers is 28mm x 28 mm, size of magnetometers is 21 mm x 21 mm. The MEG system is housed within magnetic shielded room (MSR) equipped with active shielding and automated helium recycler. The electronics comprises 306 MEG channels, 12 bioamplifier channels (SAM) and 128 EEG channels. Both MEG and EEG can be recorded simultaneously, with analog high-pass filter cut-offs dc/ 0.03 Hz /0.1 Hz/ 10 Hz (-3dB corner frequency), selectable individually for each channel by software. Low passfiltering by data acquisition software. MEG system is equipped with stimulation systems (for auditory, visual, motor and sensory tasks and intercom option with microphone). For the task–related response, we have non-magnetic single-fingeroptical response pad: finger-press more, finger-lift more and trigger output. For visual stimulation, we have high -fidelity video projection system, three -panel DLP video projector, 1,400 x 1,050-pixelnative resolution, 16-bit color depth, 112 cm screen on wheels. For auditory stimulation we have non-magnetic tubal-insert earphone set, independent delivery of auditory stimuli to each ear, 80 dB pressure level, >50 dB channel separation, <1 ms jitter between triggers and stimulus onset.3D digitizer (Polhemus Fastrack) is used for the head shape recordings. For subjects/patient support, the MEG lab is equipped with subject chair, subject bed and pediatric chair. Data analysis can be performed on three LINUX workstations.

The vision of the CCORDA is to advance clinical, translational and public health research at UNMC and in the community and region.

The mission of the CCORDA is to provide expertise in the quantitative sciences, including biostatistics, epidemiology, and health services research, and to coordinate the collaborative design, planning, conduct, analysis and interpretation of laboratory, clinical, and public health research studies. In addition, the center will provide educational training opportunities for quantitative sciences graduate students and educational opportunities for public health, clinical, and translational investigators.

Small animal MRI 7T

The Animal Behavior Core at UNMC aims to provide investigators with the expertise, equipment, and space that is required to conduct innovative acoustic, behavioral, and cognitive research with a focus on rigor, reproducibility, and maintaining the highest standards of animal welfare.

We provide dedicated procedural space and equipment for the assessment of mouse and rat behavior, cognition, and neurological function. We support investigators through consultation, training, project development, data analysis and interpretation, and data collection.

Mouse Genome Engineering (MGE) Core Facility at the University of Nebraska Medical Center (UNMC) is one of the leading transgenic core facilities in the world because, it not only offers model generation services but, it also develops newer transgenic methods and streamlines them into services that can be easily adapted, and performed by technical staff, at any transgenic core facility for routine use.

The research staff and the director of MGE core facility, in collaboration with a similar team at the Tokai University, Japan, have developed several breakthrough genome editing methods. Two notable contributions, Easi-CRISPR (Efficient additions with ssDNA inserts CRISPR) and GONAD (Genome editing via Oviductal Nucleic Acids Delivery) that were published during the recent 5 years (2 articles each in Genome Biology and Nature Protocols) are collectively cited over 400 times, accessed over 75,000 times, and are regarded as landmark papers in the field, redefining the traditional methods of generating generically engineered mouse models. Several hundreds of core facilities around the world have adapted these simplified methods and protocols, as their routine services. Being a leader in this field, and being a role model core, MGE core has attracted dozens of collaborations, within and outside the university, and it serves investigators across the globe.

Services offered: The MGE core offers end-to-end services related to all aspects of mouse model generation and mouse molecular genetics. Services include designing, construct generation, microinjection, genotyping, breeding to segregate mosaic mice, re-genotyping F1 offspring, generating figures & writing methods section for grants/manuscripts and consultation & knowledge-sharing with the PIs' team on their model/s. The MGE Core also performs cryopreservation of mouse embryos and sperm, IVF and rederivation of cryopreserved germplasm.

Links to a few landmark papers on the mouse genome engineering methods developed at UNMC MGE core facility and in collaboration with Dr. Masato Ohtsuka, Tokai University, Japan.
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1220-4
https://www.nature.com/articles/nprot.2017.153
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1400-x
https://www.nature.com/articles/s41596-019-0187-x
https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471142905.hg1507s83

A short video about Easi-CRISPR and GONAD technologies: https://www.youtube.com/watch?v=p0QXpkoPMPY&ab_channel=UNMCEDU

Sample publications of mouse models created using the protocols and methods developed in house (e.g., Easi-CRISPR).
https://www.nature.com/articles/s41467-021-21173-9
https://www.eneuro.org/content/8/1/ENEURO.0221-20.2021
https://journals.biologists.com/dev/article/147/13/dev191015/224303/Slc26a9P2ACre-a-new-CRE-driver-to-regulate-gene
https://elifesciences.org/articles/45946
https://academic.oup.com/hmg/advance-article-abstract/doi/10.1093/hmg/ddab077/6206639
https://www.nature.com/articles/s41467-019-11962-8

https://link.springer.com/article/10.1007%2Fs12035-018-1346-8

Invited review articles relevant to mouse genome engineering technologies:
https://journals.biologists.com/dmm/article/12/1/dmm029462/3039/Generating-mouse-models-for-biomedical-research
http://www.jbr-pub.org.cn/article/doi/10.7555/JBR.35.20200197

The UNMC Flow Cytometry Facility provides flow cytometry services to investigators on and off the UNMC campus on a fee for service basis.

The University of Nebraska Epigenomics Core Facility was established to assist researchers at all university and private institutions with epigenetic analysis including DNA Methylation using Pyrosequencing and Bisulfite Sequencing, Chromatin Immunoprecipitation, High Throughput Sequencing (ChIP-Seq), Real-Time Quantitative PCR gene expression analysis, Pyrosequencing Single Nucleotide Polymorphism (SNP), and Mycoplasma Testing. The Epigenomics Core Facility is located at the Durham Research Center I on the University of Nebraska Medical Center campus and is associated with the Department of Biochemistry and Molecular Biology.