ArticleBMC research notes2017
Gene expression differences between PAXgene and Tempus blood RNA tubes are highly reproducible between independent samples and biobanks.
Article in BMC research notes, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 20 citations in OpenAlex.
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- Increased expression of individual genes in whole blood is associated with late-stage lung cancer at and close to diagnosis.Scientific reports · 2023Article
- Technical assessment of different extraction methods and transcriptome profiling of RNA isolated from small volumes of blood.Scientific reports · 2023Article
- Predicting severity in COVID-19 disease using sepsis blood gene expression signatures.Scientific reports · 2023Article
- Whole blood RNA extraction efficiency contributes to variability in RNA sequencing data sets.PloS one · 2023Article
- Transcriptomics for child and adolescent tuberculosis.Immunological reviews · 2022Review
- Pre-analytical Practices in the Molecular Diagnostic Tests, A Concise Review.Iranian journal of pathology · 2021Review
- Evaluation of RNA purification methods by using different blood stabilization tubes: identification of key features for epidemiological studies.BMC research notes · 2020Article
- Article
- Comparable type I interferon score determination from PAXgene and Tempus whole blood RNA collection and isolation systems.BMC research notes · 2019Article
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGene 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.
resultsWe 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.
conclusionsMost 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.
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