Apr 07, 2025
CosMx FFPE Microtome Sectioning
- 1Stanford University
- Human BioMolecular Atlas Program (HuBMAP) Method Development CommunityTech. support email: Jeff.spraggins@vanderbilt.edu
Protocol Citation: Joanna Bi 2025. CosMx FFPE Microtome Sectioning. protocols.io https://dx.doi.org/10.17504/protocols.io.14egn4z3mv5d/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 07, 2025
Last Modified: April 07, 2025
Protocol Integer ID: 126299
Abstract
Protocol for sectioning FFPE blocks for use with CODEX
Place the paraffin blocks on wet ice for 5-10 minutes to rehydrate
Heat up a water bath to 40º C
Insert a new blade into the microtome
Prepare Leica Bond Plus slides next to the microtome
Place a paraffin block on to the microtome and cut into it until the desired part of the sample is reached
Section the tissue at 5 μm
Place the sectioned tissue in the water bath until it flattens out
Place a prepared slide in the water bath, move it towards the tissue, and gently lift it out of the bath
Ensure that sample remains in the scan area
Change the blade (or move it so an unused portion is being used) between samples and when there is paraffin build up or chipping on the blade
Let the slides dry facing upwards at an angle
Bake overnight in a 60°C oven