dc.contributor.author | Skogholt, Anne Heidi | |
dc.contributor.author | Ryeng, Einar | |
dc.contributor.author | Erlandsen, Sten Even | |
dc.contributor.author | Skorpen, Frank | |
dc.contributor.author | Arentz Schønberg, Svanhild Margrethe | |
dc.contributor.author | Sætrom, Pål | |
dc.date.accessioned | 2017-05-30T12:01:19Z | |
dc.date.available | 2017-05-30T12:01:19Z | |
dc.date.created | 2017-04-21T10:28:06Z | |
dc.date.issued | 2017 | |
dc.identifier.issn | 1756-0500 | |
dc.identifier.uri | http://hdl.handle.net/11250/2443863 | |
dc.description.abstract | Background
Gene expression profiling from blood is sensitive to technology choices. For example, the main blood RNA collection systems—the PAXgene and Tempus tubes—differently influence RNA expression signatures. The aim of this study was to establish a common RNA isolation protocol for these two systems and investigate if it could reduce the differences in gene expression between them.
Results
We collected identical blood samples on the PAXgene and Tempus systems and retrieved blood samples from two independent biobanks—NOWAC and HUNT3—which are based on PAXgene and Tempus, respectively. High-quality RNA was extracted from both sampling systems by using their original protocols and our common modified protocol, and were profiled on Illumina microarrays. Regardless of the protocol used, we found most of the measured transcripts to be differently affected by the two sampling systems. However, our modified protocol reduced the number of transcripts that were significantly differentially expressed between PAXgene and Tempus by approximately 50%. Expression differences between PAXgene and Tempus were highly reproducible both between protocols and between different independent sample sets (Pearson correlation 0.563–0.854 across 47323 probes). Moreover, the modified protocol increased the microRNA output of the system with lowest microRNA yield, the PAXgene system.
Conclusions
Most transcripts are affected by the choice of sampling system, but these effects are highly reproducible between independent samples. We propose that by running a control experiment with samples on both systems in parallel with biologically relevant samples, researchers may adjust for technical differences between the sampling systems. | nb_NO |
dc.language.iso | eng | nb_NO |
dc.publisher | BioMed Central | nb_NO |
dc.relation.uri | https://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-017-2455-6 | |
dc.rights | Navngivelse 4.0 Internasjonal | * |
dc.rights.uri | http://creativecommons.org/licenses/by/4.0/deed.no | * |
dc.title | Gene expression differences between PAXgene and Tempus blood RNA tubes are highly reproducible between independent samples and biobanks | nb_NO |
dc.type | Journal article | nb_NO |
dc.type | Peer reviewed | nb_NO |
dc.source.journal | BMC Research Notes | nb_NO |
dc.identifier.doi | 10.1186/s13104-017-2455-6 | |
dc.identifier.cristin | 1465881 | |
dc.description.localcode | © The Author(s) 2017. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated | nb_NO |
cristin.unitcode | 194,65,10,0 | |
cristin.unitcode | 194,65,15,0 | |
cristin.unitcode | 194,14,1,0 | |
cristin.unitcode | 194,63,10,0 | |
cristin.unitname | Institutt for laboratoriemedisin, barne- og kvinnesykdommer | |
cristin.unitname | Institutt for kreftforskning og molekylær medisin | |
cristin.unitname | Utdanning stab | |
cristin.unitname | Institutt for datateknikk og informasjonsvitenskap | |
cristin.ispublished | true | |
cristin.fulltext | original | |
cristin.qualitycode | 1 | |