FFPE and frozen samples hold the specimens well. However, which one you need to choose depends on your application. FFPE samples can be stored at room temperature, which is available and inexpensive and is well suited for immunohistochemical staining and morphological analysis.
FFPE is also widely used and there is a large archive of such examples for users to choose from. However, formaldehyde is toxic and the procedure for repairing and introducing paraffin takes a long time.
FFPE samples are generally unsuitable for molecular analysis and the FFPE protocol is non-standard. Therefore, there is no guarantee that different frozen tissue samples will be produced in the same way.
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The advantage of freezing is that it is faster than that of FFPE sample preparation and the sample obtained is suitable for molecular analysis.
However, because frozen specimens spoil quickly at room heat, they must be frozen as soon as possible after collection. And they need to stay frozen, which means you need a special place to freeze them.
For molecular analysis, including working with DNA, RNA, and post-translational protein modification (PTM), frozen samples are preferred over FFPE samples for several reasons.
There are situations where an FFPE sample falls behind a frozen sample for morphological testing: if you want to study the natural morphology of the tissue – or get as close to the physiology as possible, frozen samples are best.
