Aug 09, 2023

Public workspaceFFPE RNA Quality Evaluation (Qiagen) -- University of Minnesota TMCs

DOI
dx.doi.org/10.17504/protocols.io.8epv5j4x5l1b/v1
  • Qiagen1,
  • Laura J Niedernhofer2,
  • David A Bernlohr2
  • 1Qiagen;
  • 2University of Minnesota Medical School, Minneapolis, MN USA
Mickayla DuFresne-To
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DOI: dx.doi.org/10.17504/protocols.io.8epv5j4x5l1b/v1
Protocol Citation: Qiagen, Laura J Niedernhofer, David A Bernlohr 2023. FFPE RNA Quality Evaluation (Qiagen) -- University of Minnesota TMCs. protocols.io https://dx.doi.org/10.17504/protocols.io.8epv5j4x5l1b/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: May 03, 2023
Last Modified: August 09, 2023
Protocol Integer ID: 81377
Keywords: RNA, FFPE, QC, UMN
Funders Acknowledgement:
NIH - MN TMC
Grant ID: 1U54AG07041-01
NIH - MM TMC
Grant ID: 1U54AG079754-01
Abstract
Completed prior to going through -omics and spatial technologies to evaluate FFPE blocks for their RNA quality.
Before start
Evaluate if this is required for processing with your platform/technology. Not all require a certain DV200 to move forward with processing.

If tissue sample is scarce or rare, consider the best step -- Use some of the sample for RNA quality evaluation or move forward without it, understanding the risks and/or benefits of doing so.
Qiagen Protocol:
Download Qiagen RNeasy FFPE Handbook.pdfQiagen RNeasy FFPE Handbook.pdf

Qiagen product website: https://www.qiagen.com/us/products/discovery-and-translational-research/dna-rna-purification/rna-purification/total-rna/rneasy-ffpe-kit
Cat. No. / ID: 73504

Qiagen Support contact form: https://www.qiagen.com/us/knowledge-and-support/~/link.aspx?_id=5402A118CD214AF7ADBAC65422659A71&_z=z

Time needed: ~2-4 hours, depending on number of samples
Overview of RNA isolation from FFPE

Preparation of Samples for Processing
Preparation of Samples for Processing
Create or request curls from the FFPE blocks (typically done by histologist).
Follow recommendations as noted below.
Keep curls in a 1.5mL tube at -80ºC until RNA isolation process.


Once RNA isolation complete
Once RNA isolation complete
Complete:
Nanodrop for RNA quantification
DV200 for (Eukaryotic total) RNA qualification