Comparison Study of Microarray and RNA-seq for Differential Expression

Details

• Creators:
  Munster, Susan K. ; White, Vicky L. ; Hutchings, David C. ; Burian, Dennis M. ; Nicholson, Scott J.
• Corporate Creators:
  United States. Department of Transportation. Federal Aviation Administration. Office of Aviation. Civil Aerospace Medical Institute ; Venesco LLC
• Corporate Contributors:
  United States. Department of Transportation. Federal Aviation Administration. Office of Aviation. Office of Aerospace Medicine
• Subject/TRT Terms:
  • Cost effectiveness
  • Benefit cost analysis
  • Technology assessment
  • Biology
  • Blood analysis
  • Brain Microarray
  • total RNA-seq
  • differential expression
• Publication/ Report Number:
  DOT/FAA/AM-20/09
• Resource Type:
  Tech Report
• Geographical Coverage:
  United States
• Corporate Publisher:
  United States. Department of Transportation. Federal Aviation Administration. Office of Aviation. Civil Aerospace Medical Institute
• 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.
• Content Notes:
  CAMI Aerospace Medical Research Division Project No. 2017-AAM-612-GEN-10020
• Format:
  PDF
• Download URL:
  https://rosap.ntl.bts.gov/view/dot/57069/dot_57069_DS1.pdf
• File Type:
  [PDF - 2.19 MB]
• Collection(s):
  FAA Civil Aerospace Medical Institute
• Main Document Checksum:
  urn:sha-512:6411dfa4e22bbb95577dc84379bd74698e280719f4260d83650aab0bbaa408ae4199e158196fea1e44abe7fe52d5db0cbb8a1653e95682a07cb89ed21f01e6bc