Mar 31, 2026
FFPE Sectioning
- Joanna Bi1
- 1Stanford University
- Human BioMolecular Atlas Program (HuBMAP) Method Development CommunityTech. support email: [email protected]
Protocol Citation: Joanna Bi 2026. FFPE Sectioning. protocols.io https://dx.doi.org/10.17504/protocols.io.4r3l2dz6qg1y/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: March 31, 2026
Last Modified: March 31, 2026
Protocol Integer ID: 314143
Keywords: ffpe sectioning general protocol for formalin, embedded tissue, ffpe sectioning general protocol, ffpe sectioning, paraffin, formalin, assay
Abstract
General protocol for formalin-fixed, paraffin-embedded tissue. Notes on additional modifications for some assays are included.
Troubleshooting
Set up microtome with the appropriate blade
Set up water bath at 40-42°C
If the FFPE block is untouched, place the block in the specimen clamp and section (10-20 um) until tissue is exposed.
Place block face down on an ice bath. Incubate around 15 minutes or until the block surface is smooth
Place block into the specimen clamp and align with the blade.
Section block at 5um or whatever thickness necessary.
Using paintbrushes, transfer sections to water bath, and then onto a slide. Lift the slide sideways and up out of the water, making sure that there are no air bubbles.
Let the slide dry at room temperature for 30 minutes.
Known modifications
CyCIF: Use Fisher Superfrost Plus slides or equivalent charged slides with sharp corners. Make sure that the tissue is positioned along the x and y-axes as much as possible (avoid diagonal placement). Store slides in a dessicator at room temperature after drying.
Thick CyCIF: Same as CyCIF, but section at 25 um.