Decellularization and antibody staining of mouse tissues to map native extracellular matrix structures in 3D

Research output: Contribution to journalArticle


The extracellular matrix (ECM) is a major regulator of homeostasis and disease, yet the 3D structure of the ECM remains poorly understood because of limitations in ECM visualization. We recently developed an ECM-specialized method termed in situ decellularization of tissues (ISDoT) to isolate native 3D ECM scaffolds from whole organs in which ECM structure and composition are preserved. Here, we present detailed surgical instructions to facilitate decellularization of 33 different mouse tissues and details of validated antibodies that enable the visualization of 35 mouse ECM proteins. Through mapping of these ECM proteins, the structure of the ECM can be determined and tissue structures visualized in detail. In this study, perfusion decellularization is presented for bones, skeletal muscle, tongue, salivary glands, stomach, duodenum, jejunum/ileum, large intestines, mesentery, liver, gallbladder, pancreas, trachea, bronchi, lungs, kidneys, urinary bladder, ovaries, uterine horn, cervix, adrenal gland, heart, arteries, veins, capillaries, lymph nodes, spleen, peripheral nerves, eye, outer ear, mammary glands, skin, and subcutaneous tissue. Decellularization, immunostaining, and imaging take 4-5 d.


  • Alejandro E Mayorca-Guiliani
  • Oliver Willacy
  • Chris D Madsen
  • Maria Rafaeva
  • Stefanie Elisabeth Heumüller
  • Felix Bock
  • Gerhard Sengle
  • Manuel Koch
  • Thomas Imhof
  • Frank Zaucke
  • Raimund Wagener
  • Takako Sasaki
  • Janine T Erler
  • Raphael Reuten
External organisations
  • University of Cologne
  • University of Copenhagen
  • University Hospital of Cologne
  • Orthopaedic University Hospital Friedrichsheim
  • Oita University
Research areas and keywords

Subject classification (UKÄ) – MANDATORY

  • Microbiology in the medical area
Original languageEnglish
Pages (from-to)3395–3425
JournalNature Protocols
Early online date2019 Nov 8
Publication statusPublished - 2019 Dec
Publication categoryResearch