Nov 27, 2024

Public workspaceFFPE Sample Collection, Processing, and Embedding

DOI
https://dx.doi.org/10.17504/protocols.io.36wgqd7j5vk5/v1
  • Joanna Bi1
  • 1Stanford University
  • Human BioMolecular Atlas Program (HuBMAP) Method Development Community
    Tech. support email: [email protected]
Joanna Bi
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DOI: https://dx.doi.org/10.17504/protocols.io.36wgqd7j5vk5/v1
Protocol Citation: Joanna Bi 2024. FFPE Sample Collection, Processing, and Embedding. protocols.io https://dx.doi.org/10.17504/protocols.io.36wgqd7j5vk5/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: November 27, 2024
Last Modified: November 27, 2024
Protocol Integer ID: 113018
Keywords: ffpe sample collection, embedded sample, ffpe, embedding protocol, embedding formalin, processing, sample, fixed paraffin, paraffin, snyder lab, formalin
Abstract
Protocol for collecting, processing, and embedding formalin fixed paraffin embedded samples used in the Snyder Lab and Stanford University.
Troubleshooting
Sample Collection
Sample is collected fresh and kept on ice until the next step.
Clean samples and cut into pieces that fit into a tissue embedding cassette.
Transfer samples into labeled cassettes and place in 10% neutral buffered formalin for at least 24 hours.
Transfer samples (still in cassettes) into 70% ethanol until the next step.
Tissue Processing
Follow the following settings with adjustments made to the time for tissue size
BathTime
70% EtOHAny
85% EtOH1 hour
95% EtOH1 hour
100% EtOH1 hour
100% EtOH1.5 hours
100% EtOH2 hours
Xylene1 hour
Xylene1 hour
Empty5 min
Paraffin (60°C)1 hour
Paraffin (60°C)1 hour
Paraffin (60°C)1 hour

Transfer the cassettes with the samples to an embedding station
Embedding
Place the cassettes into a hot paraffin bath.
Working one sample at a time, add a small amount of melted paraffin into the bottom of the embedding mold
Place the sample into the mold in the desired orientation.
Pour more melted paraffin on top
Place the cassette flat side down on top of the mold and add enough melted paraffin to cover the slats of the cassette
Move the mold and cassette to a cooling station, fridge, or ice block.
Remove the block and cassette from the mold once fully cooled.