May 28, 2026

National Biobank standard protocol for processing PAXgene blood RNA tubes in Dutch University Medical Centers

This  protocol  is a draft, published without a DOI.
  • Yvonne D. Krom1,2,
  • Jessica C. de Greef3,
  • Ellis Niemantsverdriet4,
  • Jörg Hamann5,6,
  • Wim Timens7,
  • Peggy Manders8,
  • Hilde Brouwers9,
  • Liesbeth Niemans10,
  • Chiel de Theije11,
  • Roger R. Snijder4
  • 1Department of Neurology, Leiden University Medical Center, Leiden, the Netherlands;
  • 2Duchenne Center Netherlands;
  • 3Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands;
  • 4LUMC Biobank Organization, Leiden University Medical Center, Leiden, The Netherlands;
  • 5Department of Experimental Immunology, Amsterdam Institute of Immunology and Infectious Diseases, Amsterdam University Medical Center, Amsterdam, the Netherlands;
  • 6Neuroimmunology Research Group, Netherlands Institute for Neuroscience, Amsterdam, the Netherlands;
  • 7Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands;
  • 8Radboud Biobank, Radboud University Medical Center, Nijmegen, The Netherlands;
  • 9Central Biobank Erasmus MC, Erasmus MC, Rotterdam, The Netherlands;
  • 10Central Biobank UMC Utrecht, UMC Utrecht, Utrecht, The Netherlands;
  • 11Central Biobank MUMC+, Department of Central Research Facilities (COV), Maastricht University, Maastricht, the Netherlands
Yvonne D. Krom
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External link: https://openbioresources.metajnl.com/articles/10.5334/ojb.23
Protocol Citation: Yvonne D. Krom, Jessica C. de Greef, Ellis Niemantsverdriet, Jörg Hamann, Wim Timens, Peggy Manders, Hilde Brouwers, Liesbeth Niemans, Chiel de Theije, Roger R. Snijder 2026. National Biobank standard protocol for processing PAXgene blood RNA tubes in Dutch University Medical Centers. protocols.io https://dx.doi.org/
Manuscript citation:
Manniën, J., Ledderhof, T., Verspaget, H.W., Snijder, R.R., Flikkenschild, E.F., van Scherrenburg, N.P.C., Stolk, R.P. and Zielhuis, G.A. 2017 The Parelsnoer Institute: A National Network of Standardized Clinical Biobanks in the Netherlands. Open Journal of Bioresources 4: 3,  DOI: https://doi.org/10.5334/ojb.23
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 28, 2026
Last Modified: May 28, 2026
Protocol  Integer ID: 318108
Keywords: RNA from whole blood, processing RNA, processing of RNA, whole blood sample, RNA, whole blood, processing, blood, standard operating protocol, protocol, biobank of Dutch academic centers, Dutch academic centers, biobank, lumc biobank, national biobank standard protocol, lumc biobank facility, local biobank, biobank regulation, clinical data, national biobank, processing paxgene blood rna tube, tissue sample, store biomaterial, biobank information management system, paxgene blood rna tube, dutch university medical center, technology improvements in sample processing, downstream data use, biomarker analysis, lumc it department under supervision, dna, potential impact on biomarker analysis, lumc it department, national standard, sample processing, accordance with gdpr, data, dutch academic center, standard protocol, gdpr, blood derivate, storage of all material
Abstract
As of 2007, the 8 Dutch University Medical Centers (UMCs) have agreed to collaborate in, and exchange knowledge regarding, setting up local biobanks, where materials for a wide variety of diseases were collected under the same protocol. These nation-wide protocols are, to a large extent, still in place for most materials collected in the extant 7 UMC biobanks. Materials collected comprise blood derivates, DNA, urine, and tissue samples.
All materials and data are handled in accordance with GDPR (AVG) and Biobank regulations. Researchers may request human body material and/or clinical data.
At LUMC, the protocols to collect and store biomaterials according to national standards have been refined over the years, for example, through technology improvements in sample processing. Registration and storage of all materials is carried out in the Biobank information management system, Sample Navigator. All materials intended for scientific research are assigned a unique code that cannot be traced to the donor without access to Sample Navigator. Access is strictly governed by the LUMC IT department under supervision of the LUMC Biobank Facility.
All pre‑analytical deviations are systematically documented at the sample level to ensure transparency, reproducibility, and high‑quality downstream data use. Deviations are recorded using predefined categories, each accompanied by structured metadata and optional free‑text clarification. This enables traceability, supports FAIR data principles, and allows researchers to assess potential impact on biomarker analyses or clinical interpretation.
This protocol describes the procedure for processing PAXgene blood RNA tubes, used by the Biobank of all Dutch academic centers.
Materials
  • PAXgene blood RNA tube
Safety warnings
Treat all blood samples as potentially infectious. No hazardous substances are used.
Ethics statement
Sample collection under this protocol may only be performed with prior approval from the user’s Institutional Ethics Board (or equivalent ethics committee) and only when patients have provided informed consent for the specific biobank.
Procedure
2.5 ml whole blood is collected in a commercially available PAXgene blood RNA tube.
The PAXgene blood RNA tube is processed within 4 hours after collection.

Before initiating sample processing (and within 4 hours after collection), the PAXgene blood RNA tube is inspected for pre‑analytical deviations. The following deviation categories are captured for the tube, each accompanied by a free‑text field for additional notes:
  • Incorrect storage temperature prior to processing
  • Deviated storage duration prior to processing
The PAXgene blood RNA tube is then stored in a upright position at -20°C until 5 pm, at which time the tube is stored in a UHT freezer at -80°C.

After completion of the storage procedure, an additional pre‑analytical deviation related to the processing phase is recorded. The following deviation category is captured for the sample, with a free‑text field for additional notes:
  • Storage incident
Protocol references
Manniën, J., Ledderhof, T., Verspaget, H.W., Snijder, R.R., Flikkenschild, E.F., van Scherrenburg, N.P.C., Stolk, R.P. and Zielhuis, G.A. 2017 The Parelsnoer Institute: A National Network of Standardized Clinical Biobanks in the Netherlands. Open Journal of Bioresources 4: 3,  DOI: https://doi.org/10.5334/ojb.23