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Related Concept Videos

Fixation and Sectioning01:03

Fixation and Sectioning

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Two basic types of preparation are used to visualize specimens with a light microscope: wet mounts and fixed specimens.
The simplest type of preparation is the wet mount, in which the specimen is placed in a drop of liquid on the slide. A liquid specimen can be directly deposited on the slide using a dropper. Solid specimens, such as skin scraping, can be placed on the slide before adding a drop of liquid to prepare the wet mount. Sometimes the liquid is simply water, but stains are often added...
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Related Experiment Video

Updated: Dec 11, 2025

Proteomic Sample Preparation from Formalin Fixed and Paraffin Embedded Tissue
09:20

Proteomic Sample Preparation from Formalin Fixed and Paraffin Embedded Tissue

Published on: September 2, 2013

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Protoblock - A biological standard for formalin fixed samples.

Yensi Flores Bueso1,2,3, Sidney P Walker1,2,3,4, Glenn Hogan1,2

  • 1CancerResearch@UCC, University College Cork, Cork, Ireland.

Microbiome
|August 24, 2020
PubMed
Summary
This summary is machine-generated.

A novel Protoblock standard was developed to address limitations in analyzing DNA from formalin-fixed, paraffin-embedded (FFPE) tissues. This tool helps researchers validate FFPE microbiome analysis by accounting for DNA damage and contamination in FFPE samples.

Keywords:
BacteriaDNAFFPEMicrobiomeMicroscopyPCR

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Area of Science:

  • Pathology
  • Microbiology
  • Molecular Biology

Background:

  • Formalin-fixed, paraffin-embedded (FFPE) tissues are crucial for pathology but present challenges for DNA analysis due to DNA damage, low bacterial biomass, and extraction biases.
  • Reproducible microbiome research using FFPE samples requires reliable standards to ensure data validity.

Purpose of the Study:

  • To develop a biological standard, the Protoblock, for optimizing FFPE tissue-based research and DNA analysis.
  • To create a user-defined mock FFPE block that undergoes identical processing to clinical samples.

Main Methods:

  • The Protoblock system was created using formalin-fixed cells embedded in an agar matrix and then paraffin-embedded.
  • Microscopy verified cell content, while qPCR, 16S rRNA gene amplicon sequencing, and whole genome sequencing assessed DNA quantity and quality.
  • The Protoblock's capability to evaluate confounding factors in FFPE DNA analysis was validated.

Main Results:

  • The Protoblock system successfully represents biological material after FFPE processing.
  • DNA from Protoblocks was analyzed using various molecular techniques to assess its integrity and quantity.
  • The system demonstrated its utility in determining the impact of FFPE processing on DNA analysis.

Conclusions:

  • The Protoblock serves as a vital standard for FFPE tissue research, aiding in distinguishing biological variation from processing artifacts.
  • Its use enables more accurate interpretation of laboratory analysis outputs, relating them to real-world biological conditions.