Jun 15, 2026
Mouse Brain Microdissection Using a Brain Matrix
- 1VanAndelInstitute
Protocol Citation: Yue Ma 2026. Mouse Brain Microdissection Using a Brain Matrix. protocols.io https://dx.doi.org/10.17504/protocols.io.eq2lym3prlx9/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: June 15, 2026
Last Modified: June 15, 2026
Protocol Integer ID: 319195
Keywords: ASAPCRN, mouse brain microdissection, brain matrix the protocol, brain matrix, fresh tissue collection, further biochemical analysis
Funders Acknowledgements:
ASAP
Abstract
The protocol is used for fresh tissue collection and further biochemical analysis.
Materials
- Mouse brain matrix (adult mouse, 1-mm interval)
- Ice-cold phosphate-buffered saline (PBS)
- Stainless steel razor blades
- Fine forceps
- Dissection microscope
- Pre-chilled glass plate or Petri dish
- Dry ice
- Microcentrifuge tubes
- Mouse brain atlas for anatomical reference
Procedure
Mice were euthanized according to institutional animal care guidelines. Brains were rapidly removed and rinsed briefly in ice-cold PBS to remove residual blood.
Whole brains were placed in an ice-cold adult mouse brain matrix with the ventral surface facing downward and the rostral-caudal axis aligned with the matrix slots.
Coronal sections were generated by inserting razor blades into the matrix slots at 1-mm intervals. Brain slices corresponding to the regions of interest were identified using anatomical landmarks and a mouse brain atlas.
Tissue regions were micro dissected on a chilled surface. The striatum was dissected bilaterally from sections spanning approximately +1.5 to -0.5 mm relative to bregma. Ventral midbrain tissue, including the substantia nigra region, was collected from sections spanning approximately -2.5 to -4.0 mm relative to bregma.
Dissected tissues were immediately transferred to pre-chilled microcentrifuge tubes, snap-frozen on dry ice, and stored at −80°C until further processing.
Notes
All dissections were completed on ice to minimize protein degradation.
Tissue collection was performed consistently across animals using identical anatomical landmarks.