May 10, 2023

Tissue Sectioning Guidelines (FFPE) - CODEX/PhenoCycler V.1

DOI
https://dx.doi.org/10.17504/protocols.io.eq2ly7xoqlx9/v2
  • 1The Jackson Laboratory
William F F Flynn
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DOI: https://dx.doi.org/10.17504/protocols.io.eq2ly7xoqlx9/v2
Protocol Citation: Santhosh Sivajothi, Emily Soja, William Flynn, Elise Courtois 2023. Tissue Sectioning Guidelines (FFPE) - CODEX/PhenoCycler. protocols.io https://dx.doi.org/10.17504/protocols.io.eq2ly7xoqlx9/v2Version created by Santhosh Sivajothi
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: May 10, 2023
Last Modified: June 20, 2025
Protocol  Integer ID: 81669
Keywords: CODEX, CODEX slide prep, tissue sectioning CODEX, ffpe tissue sections suitable for phenocycler, preparing ffpe tissue section, tissue sectioning guideline, tissue section, phenocycler the purpose, phenocycler, tissue, ffpe, guideline, general guideline
Abstract
The purpose of this SOP is to provide general guidelines for preparing FFPE tissue sections suitable for PhenoCycler/CODEX
Materials
Standard 1” x 3” positively charged glass microscopy slides (example, SuperFrost Plus)
Tissue Sectioning Guidelines for CODEX/PhenoCycler
Prepare the microtome for sectioning. Section the tissue at a thickness of 5 μm.

Note
Do not exceed 10 μm as this will affect the autofocusing capabilities of the microscope. Avoid folds and tears in the tissue, as these artifacts will affect image quality and data analysis.

For best results, the tissue should be completely adhered to the slide with minimal tears or folds.
Gently place the tissue section in the center of the slide within the imageable area as shown in
grey rectangle below.
If tissue overlaps the boundary, proper coverslip seal will not be formed. Multiple tissues can be placed within the boundary, as long as there is no overlap of paraffin over adjacent tissues

Working area dimensions on slide for optimal tissue placement

Example of good tissue placement:

Slide with CODEX coverslip showing optimal placement of tissue section

Dry tissue sections overnight at RT
After drying, store cut slides at 4°C (for up to six months)
NOTE: Do not place any stickers or labels on the frosted end of the slide as it may interfere with coverslip adhesion. Use markers or directly print labels on the slide.