FAA Office of Aerospace Medicine
Civil Aerospace Medical Institute

Report No: DOT/FAA/AM-20/09

Title and Subtitle: Comparison Study of Microarray and RNAseq for Differential Expression

Report Date: October 2018

Authors: Munster SK, White VL, Hutchings DC, Burian DM, Nicholson SJ

Abstract: As costs for performing RNA-seq approach the costs affiliated with utilizing microarray technology, it is worthwhile to determine which methodology is the most efficient, cost effective, and accurate.

In this study, we examined the relative capacities of microarrays and total RNA-seq to detect differential gene expression between total RNA samples containing the following RNA mixtures: blood, brain, 2:1 blood:brain, and 1:2 blood:brain. Two microarray hybridization library amplification methods were compared to optimize microarray results, which were then compared to total RNA-seq results for the same samples. Bioinformatic analysis was performed using commonly accepted analysis software for microarray and RNA-seq data to determine which method produced the greatest number of significant differentially expressed genes.

It was determined that total RNA-seq outperformed microarrays in efficiency, result quality, and total numbers of detected genes and that cost was similar to utilizing microarrays for quantifying RNA expression levels from mixtures of brain and blood tissue.

Key Words: Microarray, total RNA-seq, differential expression

No. of Pages: 59