NDLI: Variation in RNA-seq transcriptome profiles of peripheral whole blood from healthy individuals with and without globin depletion

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Variation in RNA-seq transcriptome profiles of peripheral whole blood from healthy individuals with and without globin depletion

Content Provider	CiteSeerX
Author	Shin, Heesun Fishbane, Nick Ruan, Jian Zhou, Mi Balshaw, Robert Wilson-Mcmanus, Janet E. Ng, Raymond T. Mcmanus, Bruce M. Tebbutt, Scott J.
Abstract	Background: The molecular profile of circulating blood can reflect physiological and pathological events occurring in other tissues and organs of the body and delivers a comprehensive view of the status of the immune system. Blood has been useful in studying the pathobiology of many diseases. It is accessible and easily collected making it ideally suited to the development of diagnostic biomarker tests. The blood transcriptome has a high complement of globin RNA that could potentially saturate next-generation sequencing platforms, masking lower abundance transcripts. Methods to deplete globin mRNA are available, but their effect has not been comprehensively studied in peripheral whole blood RNA-Seq data. In this study we aimed to assess technical variability associated with globin depletion in addition to assessing general technical variability in RNA-Seq from whole blood derived samples. Results: We compared technical and biological replicates having undergone globin depletion or not and found that the experimental globin depletion protocol employed removed approximately 80 % of globin transcripts, improved the correlation of technical replicates, allowed for reliable detection of thousands of additional transcripts and generally increased transcript abundance measures. Differential expression analysis revealed thousands of genes significantly up-
File Format	PDF
Journal	PLoS ONE
Language	English
Access Restriction	Open
Content Type	Text
Resource Type	Article

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