The phenotyping module at the Czech Center for Phenogenomics houses a comprehensive collection of tools for the physiological and morphological assessment of experimental mice and rats in a controlled SPF (specific pathogen-free) environment. Our experienced staff offer a wide variety of standardized tests and services, including those of IMPReSS (International Mouse Phenotyping Resource of Standardised Screens), mandated by our active partnership in the International Mouse Phenotyping Consortium. Notable is our capacity for conducting comprehensive phenotyping pipelines, providing a wide breadth of clinical information per experimental animal, and thereby minimizing overall animal usage. Our mission is to support the preclinical research and development community with service of the highest professional standard.

For the time being for more details about our services, consultations, price quotations or requests submission please contact us at following email addresse: Your message will be guided to a respective person in charge.

First-time customers are required to set up an account using the registration form bellow. After receipt, an account number will be assigned. This number can then be used for initiating service requests from all divisions of CCP. Personal information and other data are not shared with third parties.

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IMPORTANT! Please download forms to your computer to fill it in a standalone version of Adobe Reader (or compatible software) – the form might not work if opened within an internet browser. Completed forms can be submitted using the submit button at the end of each document. If you do not receive your account number in one week after submission please contact us at

Biochemistry and Hematology

Head: Karel Chalupský, Ph.D. (metabolomics) & Roldan Medina de Guia, PhD (clinical biochemistry)

Biochemical and hematology phenotyping is based on robust primary screening developed under Eumorphia and EMPReSS, a European Mouse Phenotyping Resource for Standardised Screens. Phenotyping investigation includes also newest development in INFRAFRONTIER and IMPC consortia.

These tests comprise primary phenotyping pipeline. The Biochemical and hematology unit currently sets up examinations of various blood metabolites, ions, hormons, and enzymes of genetically modified mice. These data link changes of these parameters to metabolic and functional abnormalities of specific organs such as liver, kidney, and gastrointestinal tract.

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    Clinical Chemistry

    The following analytes can be measured. Each individual test requires 5 μl plasma, serum, or urine with an extra 10μl per sample needed for machine dead volume.

    Inorganic Analytes. Sodium (Na), Potassium (K), Chloride (Cl), Calcium (Ca), Inorganic Phosphorus (P), Iron (Fe), Magnesium (Mg), unbound-iron binding capacity (UIBC), Bicarbonate (HCO3),

    Organic Analytes. Urea, Uric acid, Cholesterol (Chol), HDL- Cholesterol (HDL), LDL- Cholesterol (LDL), Triglycerides (TRIG), Non-esterified Fatty Acids (NEFA), Glucose (GLU), Total Protein (TPRO), Albumin (ALB), Creatinine (Cr), Lactate, Conjugated and Unconjugated Bilirubin, Ferritin, Transferrin, C Reactive Protein (CRP),

    Enzymes. a-Amylase, Aspartate-Aminotransferase (AST), Alanine-Aminotransferase (ALT), Alkaline Phosphatase (ALP), Hydroxybutyrate Dehydrogenase (HBDH), Lactate-Dehydrogenase (LDH), Lipase, Creatine Kinase (CpK)



    Complete Blood Count. Our hematology test requires 25 μl of EDTA-whole blood per sample. The parameters that are measured are red blood cell count (RBC#), white blood cell count (WBC#), platelet count (PLT), hemoglobin (HGB), hematocrit (HCT), mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), red cell distribution width (RDW), mean platelet volume (MPV).

    Complete Blood Count with Differentials. This requires the same amount of EDTA-whole blood per sample and measures all the parameters in the standard test, but also includes absolute and differential cell counts for neutrophils (Neu#, Neu%), lymphocytes (Lym#, Lym%), monocytes (Mon#, Mon%), eosinophils (Eos#, Eos%), and basophils (Bas#, Bas%).

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    Multiplex Immunoassays

    The Bio-Plex multiplex reader employs magnetic bead-based immunoassays to simultaneously measure the levels of up to 100 different biomolecules in a single sample. Samples can range from serum and plasma to tissue culture supernatants. We currently offer measurements for the following molecules, and can design custom assays for new molecules.

    Adiponectin, Amphiregulin, Amylin, Betacellulin, CD40L, Cortisol, C-Peptide 2, Eotaxin, EPO, Estradiol, Exodus-2, Fractalkine, bFGF, G-CSF, GM-CSF, Ghrelin, GIP, GLP-1, Glucagon, HGF, ICAM-1, IFN-γ, IGFBP1, IGFBP2, IGFBP3, IGFBP5, IGFBP6, and IGFBP7, IL-1α, IL-1β, IL-2, IL-3, IL-4, IL-5, IL-6, sIL6-R, IL-7, IL-9, IL-10, IL-12 (p40), IL-12 (p70), IL-13, IL-15, IL-17a, IL-17F, IL-18, IL-20, IL-21, IL-22, IL-23p19, IL-25, IL-27p28, IL-31, IL-33, Insulin, IP-10, KC, Leptin, LIF, LIX, MCP-1, MCP-5, M-CSF, MDC, sMet, MIG, MIP-1α, MIP-1β, MIP-2, MIP-3α, MIP-3β, PAI-1, Pancreatic Polypeptide, PDGF-BB, Progesterone, PYY, RANTES, Resistin, TARC, Thyroid Hormones T3 and T4, TIMP-1, TNF-α, sTNFR, and VEGF


    Metabolite Quantification – HPLC

    These assays currently include the measurement of amino acids, pterins, bile acids, barbiturates, and ROS adducts (malonylaldehyde and dihydroethitidium). Further Tests can be prepared on demand.

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    IMPORTANT! Please download forms to your computer for filling out.

    New Customer Account Application

    First-time customers are required to set up an account using the above form. After receipt, an account number will be assigned. This can then be used for initiating service requests from all divisions of CCP. Personal information is not shared with third parties.

    Clinical Chemistry

    Use this form to obtain a quotation for clinical chemistry requests.


    Use this form to obtain a quotation for hematology requests

    Completed forms can be submitted using the submit button at the end of each document.

    Acrobat Reader

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    Beckman Coulter AU480

    Biochemical analyser

    Mindray BC 5300 Vet


    BioRad 200 Luminex


    Agilent 1260 Infinity


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Head: Jan Prochazka, PhD

The bioimaging unit is dedicated to comprehensive morphological and functional characterization of animal models by whole-body imaging systems in vivo and ex vivo.

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    Our microCT in vivo scanner provides sensitive and high resolution 3D imaging based on X-ray projections with voxel size 9 – 35um. Our imaging set up is suitable either for in vivo or ex vivo imaging. In vivo scans can provide comprehensive 3D visualization of bones and other mineralized tissues like teeth, but also quantification of total body fat mass and lean mass (alternative to DEXA analysis). MicroCT also provides fast imaging mode for in vivo visualization of cardiovascular system and kidneys after application of contrast agents.

    Ex vivo scanning mode can be used for higher resolution imaging or use of contrast agents for imaging soft tissues (liver, kidney, hearth, neuronal tissue) or imaging fixed embryos (E9.5 – E18.5) with use of appropriate contrast agents (Iodine, PTA). For complete microCT analysis software post-processing of projection data is necessary, especially 3D reconstruction and further segmentation for visualization of morphological phenotypes. Data can be presented as static images and/or as animated 3D reconstruction movies.

    Software tool box: ITK-snap, 3D-slicer, CTvox, CTanalyser, Imaris


    Whole skeleton microCT scan is routinely used for unbiased morphological analysis of mouse mutant lines

    Body composition analysis from 3D microCT data. Mineralized tissues like bones are in green, lean tissues like organs, intestine and muscles are in yellow and all fat tissue is in purple. Volumetric parameters can be quantified and statistically evaluated.

    Figure 6. 3D image of fixed embryo after Iodine contrasting protocol

    3D image of fixed embryo after Iodine contrasting protocol

    Imaging of contrasted soft tissues is also possible with microCT. Liver were fixed and contrasted with Iodine, bile duct structure can be visualized based on differential Iodine sequestration in liver parenchyma and bile ducts.

    Segmentation of teeth within the mouse skull. Such an approach can provide important information about tissues/structure morphology within the context of the whole skull or body.

    Radiography (X-ray)

    2D radiography is the best for fast analysis of mineralized/hard tissues, with combination of rotation stage can be also combined in 3D projection. This imaging modularity is mostly recommended as background image for other modularities (luminescence/fluorescence). Combination of optical imaging and X-ray is very suitable for anatomical annotation of fluorescence or luminescence signals.

    X-ray imaging is used for anatomical annotation of tumour position discovered by fluorescence imaging.

    Whole body fluorescence imaging

    Our device is very suitable for imaging of reflected fluorescence signals which can be used for in vivo or ex vivo imaging. Even though the ex-vivo imaging provides better signal resolution, we focus mostly on application of in vivo approach in most cases. In vivo fluorescence imaging provides unique opportunities for visualization and quantification of pathological processes like inflammation, kidney function or tumour progression in longitudinal analysis.

    The ability of cells to form tumours was visualized by detection of red fluorescent protein (RFP) expressed in inoculated cell line.

    In vivo bioluminiscence detection

    Our device includes highly sensitive camera for detection of emitted photons based on enzymatic activity like luciferase or peroxidase. This approach is suitable for in vivo imaging with emphasis on high sensitivity. This imaging is frequently used for inflammation, tumour progression, metastasis or cell homing experiments. We have successfully published our imaging protocol in the study of genetic regulation of DSS colitis. We offer our knowledge for screening of potential role of given genes in the gut regeneration processes by non-invasive imaging setup for longitudinal monitoring of healing process.

    Whole body detection of luciferase reporter. Luciferase provides very high sensitivity with out non specific background, which make is suitable for less intense processes or detection of small cell populations.

    Optical projection tomography (OPT)

    Optical projection tomography is based on screening samples from multiple angles in fluorescent or transmitted light and subsequent 3D reconstruction from projection data. This imaging approach is very suitable for early stage embryos, tissues and organs. Samples need to be cleared first by special clearing protocols. For this purpose, we are preparing protocols for 3D imaging of LacZ stained samples, whole-mount in situ hybridization samples, fluorescent proteins presence or whole mount immunologically stained samples. For basic morphology analysis we provide rapid clearing BABB based protocol and detection of endogenous autofluorescence. Final data can be presented as static images and/or as animated 3D reconstruction movies. Software tool box: ITK-snap, 3D-slicer, Imaris

    Tissue clearing and large Z-stack optical sectioning

    We can offer our experience with tissue clearing and whole-mount imaging protocols employed predominantly for cre dependent fluorescence reporters (R26mT/mG) since a standard data can be presented as volume rendered static images or animated 3D reconstructions.

    The tooth germ from a E14.5 embryo, suitable reporter has been used, tissue clearing protocol followed by large Z-stack optical sectioning with confocal microscope. Dataset was 3D reconstructed and 3D rendered in Imaris.

    Histological tomography

    In collaboration with histology unit we can offer unique 3D visualization from serial histological sections. In this procedure, the entire organ or embryo is sectioned on histological slides, processed for hematoxylin or any other histological staining, every single section is digitalized and then 3D reconstructed in Voloom software. Datasets can be also processed in Bitplane Imaris for state of the art quantification analysis.

    Whole adult kidney reconstructed from 500 serial histological sections, reconstructed in Voloom and segmented in Imaris software package.


    LacZ staining

    LacZ staining method of mouse adult tissues is important part of phenotyping screen established by IMPC. The most of knockout mouse lines generated via KOMP/ EUCOMM embryonic stem cell resources have introduced the lacZ reporter gene driven by the endogenous regulatory elements of the targeted gene. The principle of this method is histochemical staining for LacZ enzyme activity which can be detected in organs, substructures, and cells in which the gene is normally expressed. LacZ expression analysis is thus crucial for understanding of the physiological functions of a gene as well as for its role in the development or progression of diseases.



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    HREM (survey potential interest)

    We are surveying interest of the scientific community in application of HREM (high resolution episcopic microscopy) in research projects. HREM is a novel 3D imaging method based on episcopic screening of serially sectioned specimens in fully automatized manner (embryos, organs). In principle, the device generates thousands of digitalized serial sections which are subsequently 3D reconstructed. The data can be presented as volume rendered static images or animated 3D reconstructions.

  • Request FormsOpen or Close

    IMPORTANT! Please download forms to your computer for filling out

    New Customer Account Application

    First-time customers are required to set up an account using the above form. After receipt, an account number will be assigned. This can then be used for initiating service requests from all divisions of CCP. Personal information is not shared with third parties.

    Bioimaging Request Form

    Use this form to obtain a quotation for bioimaging requests.

    Completed forms can be submitted using the submit button at the end of each document.

    Acrobat Reader

    Minimal requirements for use of these forms are provided by Adobe Reader, available for free via the above link. Many other PDF viewers, including Microsoft Edge, will not work.

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    Bruker In-vivo Xtreme

    Optical and X-ray small animal imaging system for high sensitivity luminescence, fluorescence, radioisotopic and radiographic imaging.

    Bruker Skyscan 1176

    High performance in vivo micro-CT scanner for preclinical research.

    Optical projection tomography

    Custom assembly based on Wong et al, 2013.

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Banner cardio final

Head: Silvia Petrezselyova, PhD

The cardiovascular unit (CPU) provides services to assess cardiovascular function in mouse and rat models. To perform rapid and in-depth analysis of the mouse or rat heart and circulatory system in both normal and disease states, we employed several state-of-art instrumentation that allows for sensitive screening of phenotypic variations.

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    Echocardiography (Echo)

    Echocardiography is used to monitor cardiac dimensions (chamber dimensions, thickness and valvular structures) and mechanics in vivo. For comprehensive evaluating cardiac structure and function we use standard two-dimensional B-mode, M-mode, PW Doppler and Tissue Doppler ultrasound. By using these techniques we routinely perform:

    • Ultrasound assessment of cardiac function in adult mice
    • Left Ventricle Function
      • Systolic and Diastolic Analysis
      • Quantify cardiovascular function (ejection fraction, fractional shortening)
    • Right Ventricle Function
      • Wall thickness
    • Vessels Assessment
      • Visualize vessel wall movement and vascular pathologies including atherosclerosis
      • Assess blood flow through vessels and valves using Pulse Wave Doppler
    • Myocardial Wall Motion
      • Quantify myocardial mechanics using Strain as an early biomarker for cardiovascular dysfunction

    The CPU has three scanheads:

    1. MS400: 28 MHz with adjustable focal length providing an axial resolution of 55 μm – used in cardiac imaging in adult mice
    2. MS550S: 44 MHz with adjustable focal length providing an axial resolution of 40 μm – used in mouse vascular, abdominal, superficial embryonic imaging and small mouse cardiac
    3. MS250: 20 MHz – used in cardiac imaging of larger mice and rat, and imaging of large tumors (< 23 mm).

    Echocardiography is typically performed in anesthetized mice (the system contains an anesthesia device that uses isoflurane); however, echocardiography is possible to do in conscious mice as well.

    Electrocardiography (ECG)

    The CPU routinely performs recording of the murine cardiac electrical activity non-invasively through the animal`s paws using the ECGenie system (Mouse Specifics, Inc.). The size and spacing of disposable footplate electrodes facilitate contact between the electrodes and the paws to provide Einthoven lead II ECG in laboratory animals. For each animal, heart intervals and amplitudes are evaluated from continuous ECG recording after 5-min acclimation period. The CPU is equipped with ECG platforms and footplate electrodes of different sizes thus allowing ECG monitoring of mice and higher rodents, including newborn pups.

    Blood pressure

    We provide accurate tail-cuff blood pressure measurement in mice using the CODA 8-channel High Throughput Non-Invasive Blood Pressure system (Kent Scientific). The CODA utilizes volume-pressure recording technology to detect changes in tail volume that correspond to systolic and diastolic blood pressures. Blood pressure measurements are made in conscious animals maintained in normal housing conditions with minimal handling and restraint of the animals. This reduces stress levels and physiological disturbances in blood pressure measurements over a longer period whereby data quality is improved. The CPU is equipped with two CODA systems, thus the measurement can be done on up to 16 mice or rats simultaneously. The method enables accurate blood pressure phenotyping in rodents for linkage or mutagenesis studies, as well as for drug testing experiments requiring high-throughput blood pressure measurements.

    Two-dimensional (2D) ultrasound imaging. (a) – Representative B-mode echocardiographic image of an adult mouse heart. LV = left ventricle, Ao = aorta. (b) – Color Doppler ultrasound image shows renal arteries and veins. (c) – An example of PW Doppler recording across the transverse aortic arch. (d) – Representative B-mode image of embryonic day 15.5 fetus.

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    General echography

    While the central focus of the CPU is cardiovascular research, the techniques that are employed may also be useful to investigators in other fields, such as cancer, neurobiology and developmental biology. The Vevo 2100 ultrasound system allows imaging of numerous internal anatomic structures other than the heart and vascular system, namely: abdominal (kidney, spleen, liver, larger abdominal vessels), pelvic (bladder, ovaries, prostate) organs and other (e.g. eye, testes), including tumors.

    Fetal echocardiography

    For developmental studies, it is possible to monitor living mouse/rat embryos in uterus and follow the development of cardiac structures as well as changes in blood flow velocities in the heart and umbilical artery. An application of high-frequency probes with conventional 2-D and pulse-wave Doppler imaging of the fetus can provide excellent information on the early development of cardiac structures. M-mode imaging further provides important functional data, although, the proper imaging planes are often difficult to obtain.

    mouse fetus figure

    Ultrasound imaging of mouse fetus. (a) – B-mode image of embryo at embryonic day 14.5 and with an example showing either (a`) – Pulse Wave Doppler signal in aorta or (a“) – in Dorsal aorta. (b) – Magnified view of the echogenic (brighter; due to nucleated blood cells) embryonic heart.

    ECG on neonatal mice

    We use a non-invasive system (LifeSpoonTM; Mouse Specifics, Inc.) to characterize the postnatal maturation of the cardiac electrical conduction system of conscious neonatal mice. The system allows to monitor ECG abnormalities in newborn animals from day 1 of their life.


    For many studies, multiple measurements can be coordinated with the other Units of the CCP: for example, non-invasive serial echocardiographic and blood pressure determinations during a period of high-fat feeding or other environmental stress, heart rate and ECG monitoring during challenge/stress tests, and histologic evaluation on sacrifice.


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    Technology Platforms

    Vevo 2100 High-Frequency Ultrasound System (VISUALSONICS)

    Kent Coda 8 blood pressure monitor system (Kent Scientific)

    ECGenie electrocardiogram recording system (Mouse Specifics, Inc.)

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Head: Jan Procházka, PhD

The embryology unit focuses on systematic analysis of gene role in embryonic development and identification of critical period, where the phenotype is established. To achieve this unit is tightly connected to Bioimaging unit and uses state of art imaging methods (OPT, high resolution microCT, Clarity system and confocal imaging) and image analysis (Imaris) to characterize developmental phenotype in great details. Embryology unit is also well experienced in design and analysis of conditional KO mutants with use of multiple cre expressing lines and suitable fluorescence cre reporter systems.

The developmental biology is very diverse field and every project needs specific design and strategy. We are very happy to provide such a consulting before initiation of your project and prepare tailor-made experiments to follow and fulfill highest standards in the developmental biology field.

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    Embryology Services

    Cre zoo

    Cre zoo in CCP (image courtesy of Embryology unit staff)

    Whole embryo and placenta isolation/dissection. Embryos can be dissected from E5.5 in following half day intervals up to E18.5. The genotyping of embryos and resorptions are among standard procedures and harvested material can delivered up to request (fresh, frozen or fixed). The embryos can be obtained also from conditionally inactivated gene models, where gene ablation design is discussed first.

    Staining for ß-galactosidase activity. Transgenic embryos and placentas carrying a lacZ expression construct can be used for whole-mount ß-galactosidase staining. From E12.5 is the staining done one dissected organs or frozen sections in order to minimize problems with substrate penetration in larger embryos.

    Immunohistochemistry and In situ hybridization staining. Expression of RNAs or proteins can be detected using in-situ hybridization or immunohistochemistry respectively. Both can be performed either in whole mount or on sections and followed by 3D imaging methods.

    Histochemical visualization of embryonic skeletons. From 12.5 dpc onwards, the mouse skeleton can be visualized using the histochemical stains alcian blue (which stains the cartilaginous skeleton) and alizarin red (which stains mineralized tissues).

    Embryo imaging and image analysis. We use multiple imaging modalities for detail phenotype analysis in embryos of all developmental stages. We use combination of standard and high resolution microCT techniques for detail morphology and anatomy analysis, further image segmentation approaches can be used for quantification and presentation of phenotype in direct publication quality. Another imaging modality is detection of fluorescence where we use multiple tissue clearing protocols (Scal/a2, Cubic, BABB, Clarity) with combination with deep tissue imaging techniques (Light Sheet microscopy, Two-photon confocal imaging, Optical tomography and Structued illumination microscopy). For image analysis we can offer Imaris analytical station with appropriate modules for developmental biology (filament and particle tracking, Matlab extension)

    Embryonic fibroblasts (MEFs) can be readily isolated from mouse embryos 9.5 dpc and older.

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    IMPORTANT! Please download forms to your computer for filling out.

    New Customer Account Application

    First-time customers are required to set up an account using the above form. After receipt, an account number will be assigned. This can then be used for initiating service requests from all divisions of CCP. Personal information is not shared with third parties.

    Embryology Request Form

    Use this form to request services from the CCP Embryology Unit

    Completed forms can be submitted using the submit button at the end of each document.

    Acrobat Reader

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Head: Marcela Palkova, PhD

The Vision Unit is dedicated to the detection of various abnormalities in mouse sight. The current equipment of the unit enables us to analyze abnormalities in eye morphology and eye physiology.

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    Optical Coherence Tomography.

    This non-invasive imaging procedure is used to examine the posterior part of the eye (retina and retinal blood vessels). An anaesthetised animal is placed on a platform and the spectral domain OCT, integrated with confocal scanning laser ophthalmoscopy (cSLO), is used to produce a detailed cross-sectional image of the retina and retinal blood vessels. This approach enables us to detect and analyze a wide range of mouse retinal pathologies, including changes in retinal thickness and layering, and in retinal vessel number or localisation. It is also possible to assess dynamic processes like edema formation or retinal degeneration.

    Representative images acquired by OCT-device (Heidelberg-Engineering).

    Fundus picture of the posterior pole of the mouse eye (A), an image of the retina incl. retinal layers (B) and the retinal thickness profile (C) of the fundus (cross-section line depicted in figure A).


    A retinal thickness map showing averages across 3 circular areas of the fundus: optic disc and neighbouring areas at diameters of 1,2,3 mm.

    Sample images

    Movie of a reconstructed 3D-retinal model from 49 consecutive cross-sectional images of the fundus.

    (images and video courtesy of Marcela Palkova)

    Virtual vision test.

    This behaviour test provides a non-invasive functional analysis of visual performance in mice. The OptoMotry© system uses the tracking of optokinetic head and neck movements, that are reflexive in the mouse for the screening of functional vision. In this test, a mouse stands on an elevated platform in the epicenter of an arena surrounded by computer monitors, and a camera images the behavior of the animal from above. With the changing of threshold of spatial frequency, contrast, and motion of the grating, we are able to determine the visual acquity („clarity of vision“) of the tested animal. The advantage of this test is that animals with no previous exposure to the task can be tested and the measurements can be repeated regularly. This method can provide a powerful test of visual performance in gentically modified and pharmacologically treated mice.


    Electroretinography is a non-invasive diagnostic test that measures electrical responses of retina evoked by light stimulation. An anaesthetised animal is placed on a heated table inside a full-field stimulation globe (ganzfeld) and retinal responses are obtained using active electrodes placed on the cornea and reference and ground needle electrodes placed subcutaneously in the snout and at the animals’ back, respectively. The recorded signals obtained under various light conditions, stimulation intensities and timing protocols allow to individually assess the function of different retinal cell types, rods, cones, ON-bipolar cells, and, to some extend, also ganglion or amacrine cells. The standard stimulation protocols consist of single flashes of different intensity, slow (5 Hz) and fast (30 Hz) flicker and a long pulses in both dark-adapted (scotopic) and light-adapted (photopic) conditions. If needed, the protocols can be adapted to offer specific features, in example measurement of rod adaptation kinetics or stimulation by color light.

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    Standard histological staining with hematoxylin and eosin (H&E stain) can be performed on paraffin or frozen sections of embryonic or adult mouse eyes. This primary histological staining provides basic information about eye morphology.


    Immunofluorescent (immunohistochemical) detection of specific lens and retina markers can be performed on paraffin or frozen sections of embryonic or adult mouse eyes. Analysis of specific lens or retinal markers can provide more detailed information about cell types present in these tissues and extend findings from H&E staining.

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    Cerebral Mechanics OptoMotry

    Virtual reality system for rapidly quantifying a variety of OKT (optokinetic tracking) thresholds in untrained and unrestrained small rodents.

    Roland Consult RETI-animal

    Electroretinography apparatus

    Heidelberg Engineering Spectralis

    Multimodal imaging platform for spectral domain optical coherence tomography

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Hearing & Electrophysiology


Head: Jiri Lindovsky, PhD

The auditory screens provide information about function of the auditory pathway in intact anaesthetized animals. The primary test, auditory brainstem response (ABR), is based on electrophysiological recording of the brainstem structures activity evoked by acoustic stimulation. If a suspicion of cochlear hair cells damage exists, then a test of otoacoustic emissions is recommended in addition to ABR.  The unit is equipped with a 6 m3 sound attenuated booth and advanced Tucker-Davis-Technologies auditory workstation supplemented with a high quality loudspeaker suitable for rodent experiments, which allows for generation of fully customizable sound stimuli and the recording of evoked potentials in four independent channels.

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    Auditory Function

    Auditory Brainstem Response (ABR)

    ABR is an acoustically evoked potential recorded by subdermal needle electrodes placed on the top of the animal’s head. It represents a sum of activity of neurons responsible for sound processing starting at the level of the auditory nerve, through the cochlear nucleus and the superior olivary complex, up to the inferior colliculus. During the test an animal in tiletamin-zolazepam anesthesia is stimulated by simple clicks (rectangular pulses) or by pure tones of various intensity and frequency while the evoked potentials are recorded. The basic analysis of the signal provides information about the hearing thresholds (the lowest intensity of sound that is perceived by the animal) in frequency range of 1 – 30 kHz. However, other types of stimuli can be used on deemand in case an extended frequency range is needed or spectral or intensity modulation is of interest.

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    Distortion Product Otoacoustic Emissions.

    Proper function of the cochlea, specifically the cochlear outer hair cells, can be examined by recording of the distortion product otoacoustic emissions (DPOAE). DPOAE are very week sounds produced by active vibration of the hair cells which can be registered by a sensitive microphone placed in the outer ear canal during stimulation of the cochlea by sound. Diminished or completely missing DPOAE indicate damaged or missing outer hair cells. The technique is non-invasive, however, it requires general anesthesia in animals because the stimulation-recording probe is sensitive to movements that may cause artifacts in the recorded signal.

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    Tucker-Davis Technologies System 6 ( )
    Custom-made sound booth.

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Histopathology Module Head: Dagmar Zudova, DVM, PhD
Veterinary Pathologist: Peter Makovicky, PhD;
Histologist: Jan Kucera, MSc.
GLP manager & Customer services: Sarka Suchanova, PhD

The histopathology unit is dedicated for macroscopic and microscopic analysis of pathological alterations occurring in the postnatal period of mouse models. The unit is comparing gross morphology and microscopic differences between wild-type and gene-engineered mouse models. A major task is to screen for set of pathologies connected to specific genetic status in the postnatal period using the tools and techniques of the classical and molecular pathology.

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    Gross Morphology and Tissue Processing

    Full mouse/rat necropsy with organ isolation. A complete necropsy is performed to detect and record abnormal macroscopic alterations in internal and external organs. Provided in this service are a standardized scoring table using phenotype quality ontology (PATO) terms, images of any significant gross findings, and a written report prepared by a veterinary pathologist. The following organs are fixed, trimmed, processed and embedded in paraffin blocks: adrenal gland, heart, mammary gland (F), skin, thymus, brain, kidney, ovary (F), small intestine, thyroid, epididymus (M), large intestine, pancreas, spinal cord, trachea, esophagus, liver, prostate (M), spleen, urinary bladder, eye, lung, seminal vesicles (M), stomach, uterus (F), gall bladder, lymph node, skeletal muscle and testis (M). Additional organs can be processed by request.   

    Organ sampling and trimming. Individual organs can be processed. Unless otherwise specified, organs are processed according to the Revised guides for organ sampling and trimming in rats and mice, published in 2003 and 2004 by the Registry of Industrial Toxicology Animal-data (RITA) and the North American Control Animal Database (NACAD) groups (Exp Toxic Pathol 55: 91-106, Exp Tox Pathol 55: 413-431, and Exp Tox Pathol 55: 433-449).

    Tissue processing. By using a state-of-the-art automated vacuum tissue processor (Leica ASP6025), we are able to process and paraffin-embed specimens with the highest levels of reproducibility and quality. Where applicable, decalcification to remove mineral from bone or other calcified tissues is performed prior to processing to paraffin. If frozen sectioning is required, we embed tissues using a standard manual protocol and Optical Cutting Temperature (OCT) compound.

    Adult lacZ wholemount staining. Adult mouse tissues containing a lacZ reporter are scored for the presence of lacZ staining which is distinct from either nonspecific staining observed in wildtype control mice, or is too faint to score as present. Included in the survey are qualitative expression scoring of 105 distinct tissues, representative images for positive staining tissues, and anatomical description of those images.

    Sectioning and Staining

    Sectioning. Standard paraffin sections and frozen sections can be cut using a microtome or cryostat respectively. Users can select thickness options, section plane, and number of sections per block. 

    H&E staining. The standard primary staining procedure for all histological workflows is the hematoxylin and eosin (H&E) stain. For reproducible results with rapid turn around time, especially with large orders, we use an an automated stainer (Leica ST5020 + Leica ST5030).

    Special stains. The special stains are used to differentiate various biological constituents, including lipids, carbohydrates, amyloid and connective tissue and therefore are an informative methodology for scoring and monitoring many pathologies, including fibrosis, steatosis, amyloidosis etc. In research, the special stains represent an underutilized complement to standard immunohistochemistry and in many cases, can offer a cost-effective alternative. We currently employ the following special stains, and can perform additional stains upon request:

    PAS, PAS+Diastase, PAS+Alcian Blue, Alcian Blue pH 2.5, Mucicarmine, Reticulin, Elastic fibres, Giemsa, NASDCL, Massons Trichrome, Jones Methenamine Silver, Grocott Silver Impregnation (GMS), Pricrosirius Red, Pricrosirius Red Trichrome, Congo Red, Methyl Green – Pyronin, Chromotrope 2R – Analine Blue, and AZAN.


     CCP-Validated Antibodies. Immunohistochemistry to detect the following epitopes can be provided upon request with options for chromagen or fluorescence detection: caspase 3 (mouse), CD3 (mouse), CD31 (mouse), CK19, pan-CK (rat), HMW-CK (mouse, rat), cyclin D1 (mouse), F4/80 (mouse), glucagon (mouse), glutamine synthase (mouse), insulin (mouse), Ki67 (mouse), Pax5 (mouse, rat), PCNA (mouse), sSMA (rat), vimentin (mouse, rat), eYFP (mouse). Through use of the automated Ventana Discovery ULTRA, immunohistochemistry is performed with superior quality and reproducibility.

    Antibody Validation. Requests for immunohistochemistry using any other antibodies will first require successful completion of our antibody validation pipeline. Within this pipeline, staining procedures will be optimized and antibody specificity will be assessed.


    Slide Scanning

    Scanning slides has become essential for modern automated image analysis workflows and data sharing, as well as allowing the secure archiving of important histological specimens. Our Zeiss Axioscan.Z1 is capable of both brightfield and fluorescent slide scanning (up to nine parallel fluorescence channels), and is even able to scan histotopograms (double-sized slides).

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    In Situ Hybridization

    In-situ hybridization can be performed upon request. Both fluorescence and chromogenic (DIG) detection is supported. Notable is the opportunity to support reproducible large-scale in-situ hybridization studies through use of the automated Ventana Discovery ULTRA platform.

    Analytical services

    Analysis of H&E slides. Identification of alterations in organ architecture, cell architecture and/or subcellular alterations. Alteration/lesion staging and grading (where applicable).

    Analysis of special stains. Determination of matrix alterations. Scoring of cell type and density. Scoring of cellular chemical components.

    Analysis of immunohistochemistry. Proliferation scoring. Apoptosis scoring. Customized scoring.

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    IMPORTANT! Please download forms to your computer for filling out.

    New Customer Account Application

    First-time customers are required to set up an account using the above form. After receipt, an account number will be assigned. This can then be used for initiating service requests from all divisions of CCP. Personal information is not shared with third parties.

    Histopathology Services – Request Form

    Use this form for requesting histopathology services. Therein you can choose any combination of service categories (necropsy, processing, sectioning, staining etc.) noting that combinations (workflows) and bulk orders attract discounted pricing. Upon receipt of your submission, we will provide an itemized pro-forma invoice and defined work agreement for your approval (for orders above 5000CZK incl VAT).

    Completed forms can be submitted using the submit button at the end of each document.

    Acrobat Reader

    Minimal requirements for use of these forms are provided by Adobe Reader, available for free via the above link. Many other PDF viewers, including Microsoft Edge, will not work.

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    Tissue processing

    Leica ASP6025 The most modern single retort vacuum tissue processor


    Slide staining

    Leica ST5020 Multistainer + Leica CV5030 fully automated glass coverslipper

    Ventana Benchmark Special Stains Automated slide stainer for special stains

    Ventana Discovery ULTRA Automated stainer for immunohistochemistry and in situ hybridization


    Microscopy and analysis

    Carl Zeiss Axio Imager.Z2 motorized microscope imaging station, capable of both brightfield and fluorescence capture, Z-stack acquisition, tile acquisition and deconvolution.

    Leica DM3000 Semi automated high-throughput brightfield microscope system equipped with state-of-the-art color camera.


    Slide scanning

    Carl Zeiss Axio Scan.Z1 Combined brightfield and fluorescence slide scanner with ability to also scan histotopograms. Automated scanning of up to 100 standard slides and 50 histotopograms. Equiped with ultra-fast LED fluorescent module and 7 different excitation/emission filters.

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Head: Jana Balounova, PhD

The Immunology unit is taking part in the revealing of the etiopathogenic mechanisms of the immunological diseases using the transgenic mouse model. Generally, immunological disorders comprise the immune deficiencies, allergies, inflammatory diseases and cancerogenesis as well. The immune system functions are reflected in changes of the immune cell subpopulations and their products as cytokines, chemokines and other similar substances. The pathological changes can be registered in the afflicted organs, in responsible immune organs as well as in blood. We are able to evaluate the immune system functions by use of various immunological methods.

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    Comprehensive Immunophenotyping Panel (FACS)

    We routinely perform standard phenotypic immunological characterisation of particular immune cell populations in terms of their cellularity and phenotype using multicolour flow cytometry. Currently we offer two standardized panels for lymphoid and myeloid cell lineages. Standard list of CD antigens evaluated:


    PANEL A (T cells)

    antibody dye

    CD5 BV421

    CD4 FITC

    CD44 PE

    CD8a PE-CF594

    CD25 PE-Cy7

    CD62L APC-C7


    PANEL B (B and myeloid cells)

    CD5 BV421

    Ly6G BV421

    CD19 BV510

    Ly6C FITC

    CD21/CD35 PE

    CD11b PE-CF594

    CD11c PE-Cy7



    Fc block CD16/CD32 Purified

    Live/Dead SytoxBlue

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    Experimental Anti-Tumour Immunotherapy.

    We are open for collaborations in the field of tumour immunology and experimental anti-tumour therapy using murine models in general. We can test the efficacy of anti-tumour immuno- and chemotherapy and their combinations in various settings, using syngeneic murine models, K.O. mice, as well as tumour xenografts in immunodeficient mice. We can monitor immune responses during cancer development and therapy by a complex analysis, that involves analysis of immune cells both in the immune organs (spleen, lymph nodes) and the tumour microenvironment, cytokine levels monitoring and functional studies (cytotoxic tests, proliferation tests, immune suppression analyses) ex vivo. Notably, we have established experimental models of the minimal residual tumour disease after surgery or chemotherapy.

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    Please contact us directly at with your requests.

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    Flow cytometer designed to support cell analysis using up to 10 parameters.

    BioTek Epoch

    Microplate spectrophotometer / ELISA reader

    Tecan HydroSpeed

    Microplate washer for cells, beads and ELISAs in 96- and 384-well formats

    Nexcelom Cellometer Auto T4

    Automated cell concentration and viability counter

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Lung function

Lung banner 1

Lung Phenotyping head: vacant position – see the ad

At the lung-function unit we aim to offer complete and custom services ranging from screening of lung-function phenotypes in naïve (transgenic) animals to the complete screening of lung-pathophysiology in models of pulmonary diseases.

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    Assessment of lung-mechanics without challenge

    For the full assessment of lung mechanics without challenge, mice will be anesthetized, tracheotomised (end-point measurement) or intubated (repeated measurement) and attached to Scireq’s Flexivent FX and ventilated. We consecutively apply a series of different perturbations. The response from these perturbations is then analyzed by the software to calculate the lung mechanical parameters as described below. Measures are repeated until at least 4 valid measurements are obtained for every perturbation.

    The measurements with tracheotomy give more accurate results, compared to the results obtained with intubation, because leakage of air can be much better controlled (ligature around the trachea) and shorter tubes (less resistance) can be used with a tracheotomy. However, as the trachea can’t be closed after tracheotomy, this measurement is an end-point measurement. Measurements with intubation can be performed more than once in the same mouse.

    Deep-Inflation. During this perturbation lungs are inflated until the tracheal pressure reaches 30 cm H2O. Inspirational capacity, the volume of air which can enter the lungs, can be calculated from this pertubation. This parameter can be affected by any pathology which reduces the size of the airway lumen (e.g. airway wall thickening or edema) but also by parameters affecting the elasticity of the lungs (e.g. emphysema or fibrosis). Also the weight of the mouse has an influence on this parameter.

    SnapShot. The SnapShot is a sinusoidal perturbation of the airway pressure. The response of this perturbation is fit to the very basic ‘single compartment model’ of the lungs and airways. In this model the lungs are represented as an elastic balloon, giving the compliance, while the airways are represented as a tube, which confers resistance to the air going in and out of the lungs. The following parameters are calculated from this model: C: Dynamic compliance: a measure for the elasticity of the lung tissue. This will be typically affected in diseases like emphysema or fibrosis. E: Dynamic elastance: The elastance is the inverse of the compliance (E = 1/C) and thus represents the same phenomenon as the dynamic compliance. R: Resistance: a measure for the resistance the air encounters to enter and exit the lungs, which is typically increased in cases of airway narrowing and bronchoconstriction, typical landmarks for asthma.

    Quick-Prime-3 and Prime-8. Both perturbations are multi-frequency perturbations. The Quick-prime-3 takes 3 seconds while the prime-8 takes 8. As the prime-8 perturbation is longer it allows for a more accurate determination of the lung mechanics parameters. However in mice with diseased lungs and thus reduced oxygen exchange in the lungs this perturbation can be too long, causing a drop in oxygen in the lungs and consequent breathing reflexes of the animal. In these animals the Quick-prime-3 perturbation is a better choice as the oxygen levels will not drop as severely. The response to these perturbations is fit to the ‘constant phase’ model of the lungs. The advantage of this model is that one can make a difference between the resistance encountered in the central large airways and in the lung tissue (small airways and alveoli). This is interesting in disease where the central airway is not particularly affected while the small airways are, like in case of emphysema and fibrosis. The following parameters are calculated: Rn: Newtonian resistance: This parameter represents the resistance the air encounters in the central airways. Tissue damping (G): The tissue damping is a measure for the air resistance in the small airways and alveoli. Tissue elastance (H): The tissue elastance is closely related to the dynamic elastance calculated in the ‘single compartment model’ from the SnapShot perturbations and is also a measure for the elasticity of the lung and is thus influenced by the same disorders as the dynamic elastance as emphysema and fibrosis.

    PV-Loops. For the pressure-volume (PV) loops the lungs are inflated in small steps of 4 cm H2O and then left in that ventilator position for 1 second before the next step until 30 cm H2O is reached after which they are deflated in the same small steps. The advantage is that, because of the slow maneuver, lungs can reach a state of quasi static equilibrium. The compliance measured this way is thus a better measure of the true compliance of the lung. However the question is if this measure is truly very relevant, as the lung will not reach this state of quasi static equilibrium in normal breathing. Due to its slow nature, PV-loops can also help to characterize lungs in fibrosis models, in which the response is usually slowed down so much that they can’t be characterized accurately with other perturbations which are relatively fast and dynamic. PV-loops can also be helpful for translational research as they are performed in humans under ventilation. We only use this perturbation to calculate the static compliance. Full analysis of these curves is not included in the standard phenotyping but can be performed upon user’s request or the curves can be sent to the customer so that they can analyze them themselves. The following parameter is obtained from PV-loops: Cst: Static compliance: As explained above this is a measure for the elasticity of the lung in a quasi-static equilibrium.

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    Assessment of lung mechanics with challenge

    As for the full assessment of lung-function without challenge, we can perform this measurement as end-point measurement, with tracheotomy, or as repeated measures, with intubation. The challenge is given by aerosol which is generated in-line with the ventilation.

    The choice between end-point and repeated measures is more critical for these experiments, as administration of the challenge compound (typically methacholine), will cause increased pressure in the lungs during ventilation and during the perturbations. To maintain integrity of the lungs and insure that we have no pressure leakage from the tube we will have to stop the registration of the dose response curves once the pressure reaches 30 cm H2O when using intubation in a survival measurement. This should not be an issue for baseline measurements in which we do not expect the pressure to increase a lot, but could be a problem if airway hyper-reactivity is already established. In case of doubts, please feel free to contact us, so that we can establish the best strategy to suit your needs.

    With the challenge one is usually interested in the peak response after each dose of methacholine. Therefore we can only use 1 type of short perturbation to measure the response, which means that the following options are available:

    SnapShots. Is the shortest perturbation we can apply and thus the best choice to characterize the peak response. However the amplitude of the SnapShot is relatively high and we can’t limit the pressure during the perturbation. We can reduce the amplitude in the higher doses, to avoid reaching the 30 cm H2O pressure limit. However this will require an additional mouse to find the right amplitude. The parameters we can measure from these perturbations are the parameters from the ‘single compartment model’ R, E and C as described above.

    Quick-Prime-3. This perturbation is slightly longer, but the maximal amplitude of the input signal is much lower, which means that we can go to higher doses of methacholine without reaching the 30 cm H2O lung integrity pressure limit. As we are using the prime wave we can measure the parameters from the ‘constant phase model’: Rn, G and H; but also the parameters from the ‘single compartment model’: R, E and C.

    Mouse Models of Pulmonary Diseases.

    Asthma Models.

    Severe OVA-Induced Asthma. This is model is one of the oldest models of asthma which gives rise to a severe form of allergic asthma in the mouse with a strong Th2 type response due to the use of alum during the sensitization phase. A schematic representation of the model is shown in figure 1. Considering the robustness of the model and the fact that it is one of the best characterized models of asthma, it is a good choice for many studies. Its weaknesses are the exaggerated Th2 response and the lack of extensive airway remodeling. Also, in some cases, the phenotype could be too strong to see effects of interventions on the model.


    Figure 1: Schematic representation of the severe OVA-induced asthma model as used by the Czech Centre of Phenogenomics.

    Mild OVA-Induced Asthma. This model, which is also driven by OVA as model allergen, gives rise to a much milder form of allergic asthma, with much milder Th2 inflammation and less severe development of airway hyper-reactivity. A schematic representation of the protocol is shown in figure 2. This model can be useful in cases that the severe model is too strong, due to high sensitivity of the used mouse strain for example. As for the severe model its Th2 response is still exaggerated and there is a lack of extensive airway remodeling.


    Figure 2: Schematic representation of the mild OVA-induced asthma model as used by the Czech Centre of Phenogenomics.

    Short House Dust Mite Model of Asthma. This model uses a natural aero-allergen which also causes asthma in humans and animals. It is generally milder than the OVA driven models but the phenotype more closely mimics the pathology of allergic asthma as observed in human asthma, with a much milder Th2 inflammatory component and a more extensive airway remodeling. The protocol is shown in Figure 3.

    Figure 3: Schematic representation of the short house dust mite asthma model as used by the Czech Centre of Phenogenomics.

    Long House Dust Mite Model of Asthma. This model induces a more severe asthma phenotype compared to the short house dust mite model. The airway remodeling is more extensive, so it is a good choice if airway remodeling is your area of interest. A schematic overview is shown in Figure 4.


    Figure 4: Schematic representation of the long house dust mite asthma model as used by the Czech Centre of Phenogenomics.

    Emphysema Model

    Elastase-Induced Model of Emphysema. The elastase model of emphysema is a fast and simple protocol to establish emphysema. It consists of just 1 oro-pharyngal instillation of elastase after which progressive emphysema is established. Despite the fact that it has a completely different etiology as the natural disease in humans it has shown to be a powerful tool to study the development of the disease once it is established. A mild form of emphysema can already be observed 3 days after the administration of elastase and will progress to GOLD stage 2 within 3 weeks of elastase treatment.

    Pulmonary Fibrosis Model

    Bleomycin-Induced Model of Pulmonary Fibrosis. The bleomycin model of pulmonary fibrosis is one of the most used pulmonary fibrosis models in rodents. As for the emphysema model it consists of only 1 oro-pharyngal application of the compound to establish the disease. A significant fibrosis can be observed 3 weeks after administration of Bleomycin. In contrast to the emphysema model this model is not a true chronic and progressive model and some recovery from fibrosis is observed in the mouse after this 3 week period.

    Acute Lung Injury.

    LPS-Induced Model of Acute Lung Injury. Acute lung injury is a common problem in intensive care patients under ventilation, as the mechanical stress of the ventilation exacerbates mild pulmonary infections to a level in which they become a serious health issue for the patient. We are not equipped for infectious studies, but acute lung injury can be induced in mice by instillation of LPS. It will cause an acute lung injury like disease, which is strongest 24 h after LPS administration and resolves within 1 week.

    Complementary Phenotyping Services

    Histopathology. Tissues from subject to lung function assessments can be fixed, processed, embedded, sectioned and stained upon request.

    Serum IgE levels can be determined using ELISA.

    Immune Cell Typing. A standard FACS procedure using 2 cocktails of antibodies allows differentiation between: Total T cells, αβ T cells, CD4+ αβ T cells, CD8+ αβ T cells, γδ T cells, NKT cells, NK cells, B cells, monocytes, granulocytes, eosinophils, CD4+ CD25+ regulatory T cells, CD4+ CD44hi CD62Llo T cells, CD4+ KLRG1+ T cells, CD8+ CD44hi CD62Llo T cells, CD8+ KLRG1+ T cells, KLRG1+ NK cells, IgD+ B cells, Ly6Chi I-A/I-Elo monocytes and Ly6Clo I-A/I-Elo monocytes.

    Inflammatory Cytokines. Multiplex bead assay can be used to accurately measure the following inflammatory cytokines:

    Panel I: IL-1a, IL-1b, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-9, IL-10, IL-12 (p40), IL-12 (p70), IL-13, IL-15, IL-17a, Eotaxin, G-CSF, GM-CSF, IFNg, IP-10, KC, LIF, LIX, MCP-1, M-CSF, MIG, MIP-1a, MIP-1b, MIP-2, RANTES, TNFa, VEGF.

    Panel II: IL-16, IL-21, IL-22, IL-25/IL-17, IL-28B, EPO, Exodus-2, Fractalkine, MCP-5, MIP-3a, MIP-3b, TARC

    Panel III: IL-20, IL-23, Il-27, IL-33, MDC, TIMP-1

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    IMPORTANT! Please download forms to your computer for filling out.

    New Customer Account Application

    First-time customers are required to set up an account using the above form. After receipt, an account number will be assigned. This can then be used for initiating service requests from all divisions of CCP. Personal information is not shared with third parties.

    Lung Function in Mice

    Requests for studies relating to lung function in mice.

    Completed forms can be submitted using the submit button at the end of each document.

    Acrobat Reader

    Minimal requirements for use of these forms are provided by Adobe Reader, available for free via the above link. Many other PDF viewers, including Microsoft Edge, will not work.

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banner metabolism 3 red

Head: Jan Rozman, PhD (head of metabolism platform) and David Paujelo Reguera, PhD (head of energy metabolism unit)

Metabolic phenotyping is part of primary rodent phenotyping pipeline. Primary screens include intraperitoneal glucose tolerance test, insulin blood level and energy expenditure measurement. These screens were developed by Eumorphia and EMPReSS, a European Mouse Phenotyping Resource for Standardized Screens. Intraperitoneal glucose tolerance test and insulin blood level are two tests focused on screening for diabetic phenotype. Energy expenditure measurement using indirect calorimetry should detect more wide spectra of metabolic abnormalities besides diabetes. All three test are currently running in CCP and additional metabolic challenges based on chow diet are available upon request.

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    Intraperitoneal glucose tolerance test (IPGTT)

    This test is used for detection of abnormalities in glucose metabolism. In human medical practice this test is performed to diagnose diabetes and metabolic syndrome. The test is similar for mice and humans; it measures the clearance of a glucose load from the body at different time points. Mice are fasted for 16h, basal glucose level is measured prior to glucose intraperitoneal injection and glucose levels are measured during the following hours. This test involves live animal experimentation and therefore a “protokol pokusu” (permit for animal experiment) is required.

    Insulin blood level

    Insulin is a peptide hormone which is an important regulator of glucose homeostasis. The level of insulin in mouse plasma is detected during terminal bleeding. Together with the intraperitoneal glucose tolerance test, an abnormal level of insulin is indicator of diabetic or metabolism related phenotype.

    Energy expenditure

    Indirect calorimetry is a noninvasive method where oxygen consumption and CO2 production over a given period of time, and in a home cage environment, is measured. The purpose of these measurements is to provide information about energy metabolism and to detect abnormalities of carbohydrate and lipid metabolism in rodents. Since oxygen and CO2 are measured simultaneously, the respiratory exchange ratio (RER) can be calculated. As activity and food and water intake are also monitored, total energy expenditure can be evaluated.

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    Pair-feeding studies

    These studies involve an experimental setup where reduced food intake or the very same dosage of drug are explored. In drug pair feeding experiments, the amount of drug eaten by the treated group each day is determined and given to a vehicle-treated ‘pair-fed’ group of animals housed under identical conditions the following day. During the whole period food and water intake are in-line monitored together with energy expenditure monitoring. Customized setup includes choice of rodent mouse or rats, diet (control, high fat etc.), drug delivery and monitoring parameters.

    High fat fed rodent model

    These experiments are designed upon request of each client. The experimental design usually includes body weight, food and water intake, blood analysis for key metabolites, body composition and finally histological analysis.

    Diabetes induced in rodent model

    Low or high doses of streptozotocin (STZ), a toxin that specifically destroys the insulin–producing β-cells of the pancreas, is used. Together with high fat diet this model mimics disturbances in patient with type 2 diabetes.

    Body composition

    See our bioimaging section.

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    IMPORTANT! Please download forms to your computer for filling out.

    New Customer Account Application

    First-time customers are required to set up an account using the above form. After receipt, an account number will be assigned. This can then be used for initiating service requests from all divisions of CCP. Personal information is not shared with third parties.

    Metabolism Request Form

    Requests for studies relating to metabolic function in mice.

    Completed forms can be submitted using the submit button at the end of each document.

    Acrobat Reader

    Minimal requirements for use of these forms are provided by Adobe Reader, available for free via the above link. Many other PDF viewers, including Microsoft Edge, will not work.

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Neurobiology and Behavior


Head: Agnieszka Kubik-Zahorodna Ph.D.

Neurobehavioural tests using transgenic animal models make it possible to understand genetic mechanisms underlying neurological and psychiatric disorders including, but not limited to, anxiety, schizophrenia, mood disorders, and Parkinson’s disease. We employ a number of tests to examine motor abilities, cognitive functions, emotion, sensory processing as well as neurological, gait, auditory, and vision impairments in transgenic mice.

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    Animal emotionality and affect

    Open Field test evaluates animal overall motility triggered by exploratory drive in a new environment. It is also used as an initial screen for general anxiety elicited in a well-lit, open unprotected space. This fully automated test is based on video tracking system.

    Elevated Plus Maze, Light/Dark Box are other tests used to evaluate animal general anxiety which are based on approach-avoid conflict. In both tests, animals are motivated to explore a new environment in search for potential food, shelter, or mating opportunities, at the same time avoiding well-lit unprotected areas (open arms, light compartment), in favour of safer ones (closed arms or dark compartment). Both tests are fully automated and based on video tracking system.

    Forced Swim Test (FST) and Tail Suspension Test (TST) both measure animal despair in un-escapable situation and are the most widely used tools in animal models of depression. Although TST and FST share a common theoretical basis, there are many differences between them. Therefore they could complement each other providing reliable unsophisticated screen of depressive-like phenotype.

    Cognitive functions

    Cued and Contextual Conditioning are based on classical Pavlovian fear conditioning, an associative learning test routinely used to study biological basis of fear, learning, and memory. Contextual, but not cued, fear conditioning is regarded as hippocampus-dependent. Although this statement is true in most of experimental designs, animals can compensate for hippocampal damage. To overcome this limitation, we also employed Context Discrimination test where intact hippocampus is critical.

    Barnes Maze test uses natural tendency of animal to avoid well-lit, open, unprotected spaces and it is applied for testing spatial learning and memory. Test is fully automated and based on video tracking system.

    Novel Object Recognition (NOR) is based on natural preference for novelty in rodents. It evaluates animal’s exploration of a novel object as a measure of working memory and attention. NOR is particularly attractive because it requires no additional appetitive or aversive reinforcement and minimum habituation and training. NOR task can be used to study short-term memory, intermediate-term memory, and long-term memory via manipulation of the retention interval.

    Spontaneous Alternation. Rodents show strong tendency to alternation between arm choices on successive trials in Y-maze. Spontaneous alternation test is a robust and quick test of exploratory behaviour and spatial working memory. Test also requires no extensive training or external reinforcement.

    Neuromotor abilities

    Beam Walking and Rotarod. Animal sense of balance and motor coordination can be evaluated in Beam Walk test and Rotarod, which also allows assessing motor learning abilities.

    Grip Strength measures maximal muscle strength of forelimbs and hind limbs on an automated grip strength meter. The test can indicate neuromuscular abnormalities.

    Gait Analysis is based on a fully automated analysis of video records of animal foot prints. Gait analysis provides not only information about motor coordination but also detailed kinematic description of animal gait. The measured parameters are animal pace, speed, foot print area/length, a number of distinct contact area, toe spread, gate angle, paw pressure, body-foot spacing, and many others. The test can be used to studding models of Amyotrophic Lateral Sclerosis (ALS), pain/arthritis, Parkinson’s disease, muscle injury model or spinal cord injury.

    Sensorimotor gating

    Acoustic Startle Acoustic Startle Reflex (SR) is an automated analysis of startle reflex in response to acoustic stimuli. The test assesses sensorimotor processing by measuring both afferent sensory information transmission and efferent motor response. The test can also serve as a primary screen for hearing impairment. The lack of sufficient sensory gating mechanism is thought to lead to an overflow of the sensory stimulation and disintegration of the cognitive functions. SR paradigm is therefore largely used to assess the effects of putative anti-psychotics and to explore possible genetic and neurobiological mechanisms of psychosis-related behaviour.

    PPI Prepulse Inhibition (PPI) is attenuation of startle response magnitude by pre-exposure to non-startling stimulus. PPI provides operational measurement of sensorimotor gating reflecting the ability of an animal to successfully integrate relevant and inhibit irrelevant sensory information. Impaired PPI is observed in schizophrenia as well as in other neuropsychiatric disorders. 

    Pain sensitivity

    Hot/Cold Plate is automated measurement of the latency for paw licking or the first observed response, e.g. jump, in response to heat or noxious cold stimulus. The response in the hot/cold-plate test is supraspinal. The modified hot/cold-plate test with dynamic plates (temperature is slowly increased/decreased from non-noxious to noxious levels) allows to measure thermal allodynia.

    Tail Flick is automated measurement of time for tail flick reflex following the exposure to a heat stimulus (IR heat beam). It is an easy and quick test to assess rodent nociception.  The Tail Flick reflex belongs predominantly to the spinal reflexes.

    Plethysmometer measures inflammatory oedema in the animal paw. It is applied to research on rheumatoid arthritis or the central development of oedema.

    von Frey Test uses locally applied blunt ended filament to animal plantar area of paw until paw withdrawal/filament bend. This is mechanical test derived from clinical procedure to assess mechanical allodynia.

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    IntelliCage is state-of-the-art equipment that allows studying animal’s cognitive processes (aversive/appetitive conditioning, memory, taste aversion and many others) and activity in social group home cage housed animals. During an experiment (days) animals are not disrupted by human presence with sole exception of bedding change when necessary. The equipment allows automated cognitive and behavioural screening of animals living in social groups with minimum experimenter contact.

    Cued and Contextual Conditioning Modifications to our standard protocol are possible for researchers interested in assessing memory extinction, relearning, etc.

    Barnes Maze Modifications to our standard protocol are possible for researchers interested in assessing memory extinction, relearning, etc.

    Rotarod Modifications of our standard protocols are available to introduce more challenging conditions.

    Startle Reflex can be a subject to study habituation, sensitization or fear potentiation.


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    IMPORTANT! Please download forms to your computer for filling out.

    New Customer Account Application

    First-time customers are required to set up an account using the above form. After receipt, an account number will be assigned. This can then be used for initiating service requests from all divisions of CCP. Personal information is not shared with third parties.

    Neurobehavior Request Form

    Use this form to obtain a quotation for behavioral experiments.

    Completed forms can be submitted using the submit button at the end of each document.

    Acrobat Reader

    Minimal requirements for use of these forms are provided by Adobe Reader, available for free via the above link. Many other PDF viewers, including Microsoft Edge, will not work.

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    Equipment include the following:


    Intellicage by NewBehaviour (TSE Systems) is a state-of-the-art equipment allowing the testing of cognitive functions of rodents in their social groups and avoiding the human factor.


    DigiGait (Mouse Specifics Inc.) is a state-of-the-art equipment for gait analysis in various challenging conditions but unified for each animal.

    Fear Conditioning System

    ANY-maze controlled Fear Conditioning system (Stoelting, Ugo Basile SRL)

    Viewer for Animal Tracking

    Viewer for tracking, recording and analyzing animal behavior (Biobserve)

    Acoustic Startle Reflex

    Equipment for testing acoustic startle reflex (Med Associates Inc.)

    Tail Suspension Cage

    Apparatus for performing the tail suspension test (Bioseb)

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MALDI imaging

MALDI specialist: Lukas Kucera, PhD

MALDI imaging unit offers the mass spectrometry technology applied to histological samples, as it enables measurements of multiple analytes in single experimental run in spatial context, correlated with histological annotations. Currently we are measuring metabolites, lipids and proteins – mainly in various histological samples (healthy tissue, tumours) but biological fluid as well (plasma, urine). The unit is equipped with state-of-the-art imaging mass spectrometer and matrix sprayer for fine-crystal sample covering which in tandem enables nearly cell-size resolution (5 µm). With connection to MALDI Biotyper ® database we can identify broad portfolio of bacteria at high speed and confidence.

Our instrument is of TOF/TOF type, so the analyte may undergo fragmentation for further species identity confirmation (LIFT technology). Imaging data are process with dedicated software for MALDI imaging datasets (SCiLS Lab).

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    We are offering complete processing of samples for MALDI imaging analysis.

    Sample processing
    With collaboration of our Histopathology Unit we are preparing histological cryo-sections from flash-frozen or paraffin-embedded tissues and placing them onto conductive histological size glass (ITO glass).



    MALDI image of Mouse Embryo E18.5. Cryocuts coated with Norharman matrix, spectra acquired in negative mode. Lipids and metabolites are merged into single image.

    Matrix spraying
    Next step in sample processing is spraying the matrix with TM-Sprayer machine in order to obtain homogenous crystal layer of matrix substance. This enables the extraction of analyte without loss of spatial resolution. Our sprayer is capable to spray virtually any matrix within broad range of conditions (matrix type and concentration, temperature, solvent composition, gas pressure) in appreciable speed.


    MALDI Image of Mouse Ovary. Cryocuts were sprayed with Norharman matrix, spectra acquired in negative mode. Different lipids are displayed as single image and as merged image, respectively.


    MALDI image of PDX. Tumour xenograft orthotopicaly implanted to colon. Sample sprayed with 9-aminoacridine matrix. Different lipids are displayed as a single and merged image, respectively.

    MALDI measurements
    Rapiflex mass spectrometer is dedicated for MALDI imaging with high speed of image acquisition (laser frequency 10 kHz) with high spatial resolution (down to 5 µm). These enable to process even large samples or many tissue cuts to be analyzed in shortest time as possible and to utilize even matrices which quickly evaporates in high vacuum (such as DHB or Norharmane). Rapiflex mass spectrometer has good sensitivity and resolution. LIFT technology may be applied for fragmentation and confirmation of sample identity.

    Data Processing
    With high speed of data acquisition and high spatial resolution of images resutling datasets may become large. SCiLS Lab software together with dedicated processing PC station are fast enough to deal this task. SCiLS Lab software offers the possibility to display the mass spectrometry imaging data, correlate the images with histological staining and performs various statistical computations on multiple sections or datasets in one run.

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    Bruker Rapiflex

    HTX TM-Sprayer

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