University of California San Diego Mouse Phenotype Service
Frequently Asked Questions

  1. It is highly recommended that you converse with a trained mouse histotechnologist for help with planning experiments that will need histology analyses. See Resources Tab.

  2. Optimum handling of mouse tissues: How does one decide whether the tissue is to be Frozen or FFPE (Formalin Fixed Paraffin Embedded)?

    Frozen sections are best used for immunohistochemistry assays, but morphologic detail is not well preserved usually. Frozen tissues that are correctly frozen with OCT compound, in a dry ice/isopentane slurry (see protocol) are cryo-sectioned in a CRYOSTAT.

    Paraffin Sections: Much better morphologic detail is obtained when examining standardly fixed, processed, stained PARAFFIN SECTIONS. It is best to label the cassettes yourself, using the indelible marker (NOT A SHARPIE, the ink of which is soluble in the solvents that are used to process the tissues into paraffin).

  3. For immunohistochemistry assays: Before embarking on time-consuming immunohistochemistry assays, it is important to confirm antibody reactivity using flow cytometry and Western Blots. This will also help the histotechnologist decide on concentration of anitbody to use when planning the immunohistochemistry assays.

    Also remember one can plan to use pellets of TISSUE CULTURE GROWN CELLS, which thus become important controls for immunohistochemistry experiments.

  4. Contact information for serum chemistry analyses at UC San Diego

  5. Contact information for analyses of muscle and peripheral nerve

  6. Multiparametric and semiquantitative scoring systems for the evaluation of mouse model histopathology

  7. Improving Tissue Sampling Profiling

  8. Mouse histology atlas

  9. Using Unfixed, Frozen Tissues to Study Natural Mucin Distribution

  10. Comparative human and mouse mammary gland and neoplasia

  11. Frozen section techniques

  12. Prepare frozen blocks

  13. Prepare formalin fixed paraffin embedded tissue blocks

  14. Mouse Necropsy protocols

  15. The Jackson Laboratory - Contact:

  16. Links to other useful information


  • Ladiges W, Ikeno Y, Liggitt D, Treuting P (2013) Pathology is a critical aspect of preclinical aging studies. Pathobiol Aging Age-Relat Dis 3:22451.
  • Brayton CF, Treuting PM, Ward JM (2012) Pathobiology of aging mice and GEM: background strains and experimental design. Vet Pathol 49:85–105
  • Sundberg J.P. et al 2011 The mouse as a model for understanding chronic diseases of aging: The histopathologic basis of aging in inbred mice. Pathobiol Ageing Age Relat Dis 2011; 1: 10.3402/pba.v1i0.7179.
  • Treuting, P.M. and Pettan-Brewer, C. Practical Pathology of aged mice. Pathobiol Ageing Age Relat Dis 2011; 1: 10.3402/pba.v1i0.7202.
  • C. Brayton 2009 Mouse Pathology Glossary Johns Hopkins Mouse phenotype core
  • Aoshiba, K., Nagai,A. Chronic lung inflammation in aging mice FEBS letters 2007.Vol 581 Issue 18 3512-3516

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