Jul 31, 2024
Sinai SCENT TMC - FFPE Blocking, Sectioning, and TMA Construction
Reserved DOI:
10.17504/protocols.io.5jyl82wjrl2w/v1
- 1Icahn School of Medicine at Mount Sinai
Protocol Citation: Sojin Kim 2024. Sinai SCENT TMC - FFPE Blocking, Sectioning, and TMA Construction. protocols.io https://protocols.io/view/sinai-scent-tmc-ffpe-blocking-sectioning-and-tma-c-dh6y39fw
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: July 31, 2024
Last Modified: July 31, 2024
Protocol Integer ID: 104376
Abstract
FFPE Blocking and Sectioning protocol
Guidelines
Comply with Universal Precautions when handling all specimens.
Use personal protective equipment according to the institution’s guidelines.
Safety warnings
Do not allow tissue samples to dry at all (One-at-a-time)
FFPE Blocking and Sectioning
FFPE Blocking and Sectioning
Rince the collected tissues in PBS to remove blood.
Place tissues in at least 10 volumes of buffered formalin or buffered paraformaldehyde
Incubate for the necessary fixation time
1. 1-2 mm thick: 2-3 hours RT
2. 5-10 mm thick: 5 hours RT
3. >10 mm thick: 2-3 hours RT with overnight at 4'C
Rinse tissue twice with PBS, and store at 4'C in 70% EtOH
Label sample ID on both the front and side of the histology cassettes
Trim and transfer the tissue in the histology cassettes. Small tissue pieces < 1-2mm should be placed between blue sponges within thecassette.
Immerse in the 70% EtOH in the storage bucket
Drop off the samples at the Biorepository and Pathology CoRE (Mount Sinai)
Sectioning thickness
- Xenium: 5 um
- Orion: 5 um
TMA Construction
TMA Construction
Donor blocks are selected by the researcher and pathologist based on study criteria.
Exclusive criteria
1. Artifacts such as folding or tearing
2. Areas with excessive bleeding
Inclusive criteria (for Lung tissues)
Alveolar, bronchial, and endothelial, while trying to select the same anatomical regions among the samples.
The region of interests are marked using the NDP.view 2 program and submit the annotated H&E scan to the Biorepository and Pathology CoRE Team at Mount Sinai.