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Series GSE103889 Query DataSets for GSE103889
Status Public on Sep 20, 2019
Title Gene Expression Profiling of Whole Blood: A Comparative Assessment of RNA-Stabilizing Collection Methods
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Peripheral Blood gene expression is widely used in the discovery of biomarkers and development of therapeutics. Recently, a spate of commercial blood collection and preservation systems have been introduced with proprietary variations that may differentially impact the transcriptomic profiles. Comparative analysis of these collection platforms will help optimize protocols to detect, identify, and reproducibly validate true biological variance among subjects. In the current study, we tested two recently introduced whole blood collection methods, RNAgard® and PAXgene™ RNA, in addition to the traditional method of peripheral blood mononuclear cells (PBMCs) separated from whole blood and preserved in Trizol reagent. Study results revealed striking differences in the transcriptomic profiles from the three different methods that imply ex vivo changes in gene expression occurred during the blood collection, preservation, and mRNA extraction processes. When comparing the ability of the three preservation methods to accurately capture individuals’ expression differences, RNAgard® outperformed PAXgene™ RNA, and both showed significantly better individual separation of transcriptomic profiles than PBMCs. Hence, our study recommends using a single blood collection platform, and strongly cautions against combining methods during the course of a defined study.
Overall design Peripheral blood was collected from eight healthy volunteers. Three comparitive groups for each subject, namely, blood preserved in PAXgene™ RNA tube, RNAgard® Blood Tube and CPT tube. Biological replicates (per subject): 3 RNAgard® Blood Tubes, 2 PAXgene™ RNA tubes and 3 CPT tubes (reference group).
Contributor(s) Donohue DE, Srinivasan S, Gautam A, Ann-Miller S, Hammamieh R, Jett M
Citation(s) 31600258
Submission date Sep 15, 2017
Last update date Jul 25, 2021
Contact name Aarti Gautam
Phone 301-619-7683
Organization name WRAIR
Department Medical Readiness Systems Biology
Street address 503 Robert Grant Avenue
City Silver Spring
State/province MD
ZIP/Postal code 20910
Country USA
Platforms (1)
GPL17077 Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray 039381 (Probe Name version)
Samples (64)
GSM2785589 207_ RNAgard tube Replicate 1
GSM2785590 207_ CPT tube Replicate 1
GSM2785591 207_ PAXgene RNA tube Replicate 1
BioProject PRJNA407417

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Supplementary file Size Download File type/resource
GSE103889_RAW.tar 373.8 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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