Animal Models & Biorepository

Expertise, resources, and facilities for animal husbandry, necropsy, and histological services for liver disease research

The primary function of this core is to provide members of the Hepatobiology & Toxicology COBRE with the expertise, resources and facilities needed for animal husbandry, necropsy and histological services for animal models of liver disease. The Core isolates primary hepatic cells (parenchymal, Kupffer, stellate, sinusoidal endothelial cells) for ex vivo and in vitro studies. The Core also facilitates cataloging and storage of animal and clinical samples in a biorepository that will provide biobanking infrastructure and support, so that other researchers may share the tissue generated by COBRE-supported projects. 

Aims of the Core

  1. To foster the development and success of proposed COBRE projects and future pilots. The Core develops and implements SOPs for the measurement of liver pathobiology. The Core also fosters translation of basic research into human studies using the Biorepository.
  2. To educate and train investigators. The Core has trained personnel who will educate individual investigators on how to correctly phenotype of hepatic injury. The Core also assists individual investigators in designing appropriate animal protocols, surgical procedures, tissue collection and storage protocols for new and ongoing projects.
  3. To develop new protocols and techniques: The Core will expand the repertoire of experimental techniques, models and infrastructure to meet the current and future needs of COBRE and non-COBRE members.
  4. To become an integral and self-sustaining component of the COBRE. The Core is a self-sustaining entity that promotes the long-term stability of the COBRE by providing essential services and developing new and unique capabilities for individual and multi-PI projects, as well as offering biobanked tissues on a fee-for-service basis to non-COBRE members.

Core Leader
Irina Kirpich, PhD, Animal Models
Matt Cave, MD, Biorepository

Facilities & Instrumentation The Animal Model and Biorepository Core (Core D) is housed in the main space of the Hepatobiology and Toxicology COBRE, on the 5ᵗʰ floor of the Clinical and Translational Research building on the Health Sciences Campus. This facility opened in the fall of 2009 and has state-of-the-art facilities for research and support.

Major Equipment

Surgical stations

The survival surgical station is equipped with a VetiEquip Isoflurane rodent anesthesia system. This is the preferred method of anesthesia for survival surgeries in rodents as induction is rapid, deep and the animals recover rapidly. The station has also 2 surgical microscopes, sterilization supplies for both consumables and for tools (Steri350 bead sterilizer), a coagulator, surgical-grade consumables (e.g., sutures), and several sets of microsurgical tools. Warming pads for surgery and recovery are also available. We also have a dedicated sacrifice station in the Core facility. This station also has a peristaltic pump (Gilson Minipuls 3) for the initial perfusion of liver with collagenase for hepatic cell isolation. The sacrifice station also has a bead-based homogenizer (Micro-Minibeadbeater-1) for rapid homogenization and extraction from tissue (e.g., for RNA).

Metabolic cages, cage racks and syringe pumps

The Core owns 42 metabolic cages and racks to house them. These metabolic cages include urine collection tubes with funnels, feces collection tubes, and a feeder chamber. These cages permit acquisition of untainted urine and feces for study (e.g., for metabolomic or metagenomic profiling). These can also be employed to measure alcohol concentrations in the urine in alcohol feeding trials. Several high-torque syringe pumps (Harvard Apparatus) are available for intragastric infusion of liquid diets; the Core houses enough pumps for all of the metabolism cages to be simultaneously occupied.

Image acquisition and analysis

The Core houses a Metamorph image acquisition and analysis system (Chester, PA) incorporating a Nikon E600 microscope with a SpotRT digital camera. This system captures high-quality bright-field and fluorescent photomicrographs. The system can also quantitate range, as well as assist in the counting of cells.

Primary cell culture hood and incubators

The facility has a cell culture room dedicated to primary cells equipped with laminar flow hoods and incubators, and a Nikon T5100 inverted microscope. This physical separation of primary cells from cultured cell lines prevents the possibility of cross-contamination.


Several centrifuges are housed in the core, including a 2 benchtop and a refrigerated microfuge for isolating/extracting samples, high speed centrifuge (an Avanti J-20 XP with elutriation rotor and 2 Avanti J26 XP-1 centrifuges with rotors), ultracentrifuges (Optima L-100 XP, Optima Max-XP or TLX centrifuges), and cell isolation centrifuges (Sorval RT+).
Embedding station and Microtomes (Leica CM1850 cryostat and RM2235)

To prepare biological tissue for observation under a microscope, the tissue is either frozen and sectioned in a cryostat or embedded in a hardening material like paraffin or resin. The use of Cryostat microtome allows the correct or precise sectioning of the specimen, trimming and accurate section thickness. Sectioning can be performed on fixed and unfixed tissue specimens. It preserves the cell morphology, texture, enzyme activity for histochemistry and antigenicity for immunohistochemistry and in situ hybridization.

Freezer farm

The Core currently houses 23 –80°C freezers in the CTRB for the use of stored biobanked samples. All of these freezers are plugged into the emergency generator line for the building and/or are attached to liquid nitrogen tank supplies, to limit the effects of any potential power outages/fluctuations.

Fee Schedule for Core Pathology Services

COBRE Mentees COBRE Non-Center Members
Tissue Processor Free $75 flat fee $150 flat fee
Embedding Unit
per sample fee
$25/hour; 2 hr minimum
$50/hour; 2 hr minimum
Microtome Free $5/hour $10/hour
Gemini Autostainer TBA TBA TBA
EchoMRI (Body Fat Composition Analysis)
Initial Training and Operation Orientation
(up to two individuals can be trained during one session)
$15/mouse; 5 mouse minimum
$30/mouse; 5 mouse minimum

Please stop by room 527E in the Clinical and Translational Research Building to see equipment and arrange a training time with Kim Head for use.