Feb 02, 2023
Version 6
OMS Atlas FFPE Spatial Mapping V.6
- 1Oregon Health & Science University;
- 2Knight Comprehensive Cancer Institute, Oregon Health & Science University
Protocol Citation: Brett Johnson, Danielle Galipeau, George Thomas 2023. OMS Atlas FFPE Spatial Mapping. protocols.io https://dx.doi.org/10.17504/protocols.io.8epv56ppjg1b/v6Version created by Brett Johnson
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: January 31, 2023
Last Modified: February 02, 2023
Protocol Integer ID: 76181
Keywords: biospecimen, FFPE, tissue processing, spatial mapping
Abstract
This protocol describes the procedure by which the OMS Atlas serially sections a FFPE block, prepares the resulting slides, and then distributes the specimens for downstream analysis.
Materials
MATERIALS
Tanner Scientific 45° White Adhesive Slide with Beveled EdgeMercedes MedicalCatalog #TNR WHT45AD
Superfrost Plus Microscope SlidesFischer ScientificCatalog #12-550-15
Tomo® adhesion slides clipped cornersVWR InternationalCatalog #10748-172
Additional equipment:
- Microtome
Before start
Transfer FFPE blocks to OHSU Knight Histopathology Shared Resource (HSR) for sectioning and processing. Coordinate execution of this sectioning protocol to allow for shipping within the same business week.
Preparation
Preparation
Verify the identity of the FFPE block to be cut against written request for sectioning.
Label all slides with a unique BEMS ID and slide number, corresponding to the written request and FFPE spatial map (below).
| A | B | C | D | |
| Slide# | Slide Type | Assay | Recipient | |
| 1 | Superfrost Plus | H&E | OHSU, HSR | |
| 2 | Superfrost Plus | Cyclic Immunofluorescence (Tumor Panel) | HMS, Alyce Chen | |
| 3 | Superfrost Plus | Cyclic Immunofluorescence (Immune Panel) | HMS, Alyce Chen | |
| 4 | TOMO | Multiplex IHC (Discovery Panel) | OHSU, Sam Sivagnanam | |
| 5 | Tanner | Cyclic Immunofluorescence (Panel A) | OHSU, Koei Chin | |
| 6 | Tanner | Cyclic Immunofluorescence (Panel B) | OHSU, Koei Chin | |
| 7 | Superfrost Plus | Nanostring GeoMx Digital Spatial Profiler | OHSU, KDL | |
| 8 | Superfrost Plus | H&E | OHSU, HSR |
Sectioning
Sectioning
Align block on microtome to minimize tissue loss.
Face into block at 5μm until full section of tissue is achieved.
Cut adequate ribbon at 5μm to cover all 8 serial sections.
Mount tissue sections onto appropriate slide types, maintaining serial order and orientation of sections.
Processing
Processing
Perform hematoxylin and eosin (H&E) staining on slides #1 and #8.
Bake slides #2, 3, 5, and 6.
Place slides #2, 3, 5, and 6 in 55 °C oven overnight.
The next morning, raise the oven temperature to 65 °C for up to 01:00:00 .
Note: Slides should be baked at 65 °C for at least 30 minutes.
Remove slides from oven. Place slides in slide boxes and store at room temperature.
Deliver slides #2 through #7 to BioLibrary for distribution.