Jun 02, 2026
Collection and preparation of colon from mice to calculate the colon index and for immunohistochemistry
- Amandine EVEN1,2,3,4,5,
- louis-eric.trudeau Trudeau1,2,3,5,4,6
- 1Department of pharmacology and physiology, Faculty of Medicine, Université de Montréal;
- 2Neural Signaling and Circuitry research group (SNC);
- 3Center for Interdisciplinary Research on the Brain and Learning (CIRCA);
- 4Institut Courtois d’innovation biomédicale;
- 5Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815;
- 6Department of Neuroscience, Faculty of Medicine, Université de Montréal
Protocol Citation: Amandine EVEN, louis-eric.trudeau Trudeau 2026. Collection and preparation of colon from mice to calculate the colon index and for immunohistochemistry. protocols.io https://dx.doi.org/10.17504/protocols.io.5jyl84z87g2w/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: April 21, 2026
Last Modified: June 02, 2026
Protocol Integer ID: 315476
Keywords: preparation of colon, colon index, immunohistochemistry this protocol, collection of colon, immunohistochemistry analysis, immunohistochemistry, colon, immunohistopathology, preparation for futur rna, futur rna, mice, index, calculation of the index
Funders Acknowledgements:
Aligning Science Across Parkinson's
Grant ID: ASAP-000525
Abstract
This protocol describes the collection of colon from mice, the calculation of the index and the preparation for futur RNA, protein, immunohistopathology or immunohistochemistry analysis.
Materials
Solutions:
- Cold PBS 1X
- Cold 4% PFA or cold formol
Materials:
- ruler
- scissors and scalpel
- precision scale for weighing the colon
- normal scale for weighing animals
- 10ml syringe
- 21G needle
- petri dish
- scalpel
- Kimwipes
- Dry ice
- a bottle and mold (if immunohistochemistry)
Tissue collection
The mouse is weighed, which is necessary for subsequent calculation of the colon index.
After an appropriate euthanasia, the caecum and the colon are dissected from the mouse.
The colon corresponds to the section between the cecum and the anus.
Measurement of the size and the colon index
The lenght of the colon is mesured with a ruler from the caecum to the end.
A photography is done with the ruler for record.
The caecum is removed.
If present, feces are carefully removed.
To do this, gently slide a forceps along the colon from the proximal to the distal part to expel the feces.
The colon is weighed with a precision scale.
The index is calculated as the colon mass (mg)/mouse body mass (g).
Cleaning
Colons are sectioned in two with a scalpel blade
- proximal portion, from the part which followed the caecum to the middle
- distal portion from the middle to the part which was connected to the anus
Each sections are washed;
Colon sections are maintained in a petri dish full of cold 1X PBS.
With a 10 mL syringe and a 21G needle, flush the inside of the colon with cold 1X PBS until it is completely clean.
Be careful not to damage the tissues. Apply a steady flow of cold PBS to distend the colon and avoid touching the tissue with the needle.
Excess 1X PBS is dried by very quickly applying the section to a Kimwipe and the tissue is stored.
Storage of the sample
For futur analyses of colon RNA or protein, sections are directly transfered into dry 2 mL tubes and transfered on dry ice. After the collection of all samples, the tubes are transfered to -80 °C .
For subsequent colon immunohistopathology or immunohistochemistry, tissues need to be fixed.
For immunohistopathology, sections are transfered into 2 mL tubes containing cold 4% PFA and are kept at 4 °C 1-2 days before embedding.
For immunohistochemistry, sections are directly inserted into a mold and transfered into a bottle of cold formalin. Bottle are kept at 4 °C 1-2 days before embedding.