<p class='jove_content'>All procedures involving human participants have been performed in compliance with the institutional, national and international guidelines for human welfare and have been reviewed by the local institutional review board.</p>
<p class='jove_title'><strong>1. Washing the Slides</strong></p>
<ol>
	<li>Prepare 10 &#181;m of unstained formalin-fixed paraffin-embedded (FFPE) sections.</li>
	<li>Place slides in a glass slide holder: use about 3-5 largest cross-sectional slides unless the tissue is minimal, and more slides are needed.</li>
	<li>Fill the slide holder with Xylene, and make sure that all tissue on the slide is submerged. Allow to sit for 15 min.</li>
	<li>After 15 min, pour out the Xylene with the slides held with a pipette tip so that the slides do not fall out.</li>
	<li>Pour in more Xylene to the same level as before. Allow to sit for another 15 min.</li>
	<li>After 15 min, pour out the Xylene again.</li>
	<li>Fill the slide holder with 100% ethanol (EtOH), and make sure that all tissue on the slide is fully submerged. Allow to sit for 3 min.</li>
	<li>Pour off the EtOH while carefully holding the slides. Refill to the same level with more EtOH. Allow to sit for 2 min.</li>
	<li>Pour off the EtOH again and remove the slide. Carefully place them face up on a clean paper towel to dry. Allow to sit for 10 min.</li>
</ol>

<table><tbody><tr><td>Xylene</td><td>&amp;nbsp;Sigma-Aldrich</td><td>214736</td><td></td></tr><tr><td>100% Ethanol&amp;nbsp;</td><td>&amp;nbsp;Sigma-Aldrich</td><td>24194</td><td></td></tr></tbody></table>

deparaffinization and rehydration of tissue sections: a two-step procedure to remove paraffin wax from ffpe tissue slides followed by tissue rehydration

Deparaffinization and Rehydration of Tissue Sections: A Two-step Procedure to Remove Paraffin Wax from FFPE Tissue Slides Followed by Tissue Rehydration

<p class='jove_content'>Source: Sugimoto, K. <em>et al</em>. <a href='https://www.jove.com/video/61355' target='_blank'>Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer.</a> <em>J. Vis. Exp.</em> (2020)</p>
<p class='jove_content'>In this video, we demonstrate the processing of FFPE or formalin-fixed paraffin-embedded sections obtained from gastrointestinal tumor tissue. The deparaffinization and rehydration steps allow the processing of the tissue specimen for subsequent analytical applications.</p>

Source: Sugimoto, K. et al. Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer. J. Vis. Exp. (2020)
In this video, we demonstrate the ...

<p>Formalin-fixed paraffin-embedding or FFPE technique allows the preservation of fixed, dehydrated, and cleared tissue specimens within paraffin blocks for long-term storage. FFPE preserves proteins and other vital intracellular components without compromising the tissue morphology.</p>
<p>Deparaffinization, or the removal of paraffin wax surrounding the embedded tissue, is a critical step before processing any FFPE tissue specimen for downstream analysis. To begin deparaffinization, start with a glass slide carrying an unstained FFPE tissue section of interest having an appropriate thickness.</p>
<p>Immerse the tissue section in a xylene bath and incubate for the desired duration. Xylene, an organic solvent, dissolves the paraffin wax that has embedded and penetrated the tissue. The complete removal of paraffin wax exposes the fixed and dehydrated transparent tissue specimen.</p>
<p>Following deparaffinization, treat the specimen with absolute ethanol. Ethanol displaces and removes any traces of xylene from the tissue section. Subsequently, immerse the tissue in decreasing concentrations of ethanol. The process rehydrates the tissue for downstream histological analysis.</p>
<p>Finally, leave the slide undisturbed for the desired duration. This step allows ethanol and water to evaporate and obtain a dry rehydrated tissue section.</p>

<p>To begin, prepare 10 micrometers of unstained formalin-fixed paraffin-embedded sections. Place the slides in a glass slide holder and fill it with xylene, making sure that all tissue on the slide is submerged. Leave the slides in xylene for 15 minutes. Then, pour out the xylene while holding the slides with a pipette tip so that they do not fall out. Pour in more xylene to the same level as before and repeat the incubation.</p>
<p>Pour out the xylene and fill the slide holder with 100% ethanol, making sure that all the tissue on the slide is fully submerged. Leave the slides in the ethanol for 3 minutes. Then, replace the ethanol with fresh ethanol and allow them to incubate for two more minutes. Pour off the ethanol and remove the slides. Carefully place them face up on a clean paper towel and allow them to dry for 10 minutes.</p>

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Research

JoVE Encyclopedia of Experiments

Cancer Research

Gastrointestinal Cancer

Assays and techniques

10.3K Views. Formalin-fixed paraffin-embedding or FFPE technique allows the preservation of fixed, dehydrated, and cleared tissue specimens within paraffin blocks for long-term storage. FFPE preserves proteins and other vital intracellular components without compromising the tissue morphology. Deparaffinization, or the removal of paraffin wax surrounding the embedded tissue, is a critical step before processing any FFPE tissue specimen for downstream analysis. To begin deparaffinization, start with...

Abstract

Protocol

Disclosures

<table><tbody><tr><td>Xylene</td><td>&nbsp;Sigma-Aldrich</td><td>214736</td><td></td></tr><tr><td>100% Ethanol&nbsp;</td><td>&nbsp;Sigma-Aldrich</td><td>24194</td><td></td></tr></tbody></table>

Deparaffinization and Rehydration of Tissue Sections: A Two-step Procedure to Remove Paraffin Wax from FFPE Tissue Slides Followed by Tissue Rehydration

In This Article

Abstract

Protocol

Disclosures

Materials

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List of materials used in this article
Name	Company	Catalog Number	Comments
Xylene	Sigma-Aldrich	214736
100% Ethanol	Sigma-Aldrich	24194