Journal of Ocular Biology, Diseases, and Informatics

, Volume 2, Issue 4, pp 243-249

First online:

Open Access This content is freely available online to anyone, anywhere at any time.

Use of bioanalyzer electropherograms for quality control and target evaluation in microarray expression profiling studies of ocular tissues

  • Christina A. HarringtonAffiliated withGene Microarray Shared Resource, Oregon Health and Science UniversityKnight Cancer Institute, Oregon Health and Science UniversityVaccine and Gene Therapy Institute, Oregon Health and Science UniversityCH14G, Oregon Health and Science University Email author 
  • , Michael WintherAffiliated withGene Microarray Shared Resource, Oregon Health and Science University
  • , Michelle M. GarredAffiliated withGene Microarray Shared Resource, Oregon Health and Science University


Expression profiling with DNA microarrays has been used to examine the transcriptome of a wide spectrum of vertebrate cells and tissues. The sensitivity and accuracy of the data generated is dependent on the quality and composition of the input RNA. In this report, we examine the quality and array performance of over 200 total RNA samples extracted from ocular tissues and cells that have been processed in a microarray core laboratory over a 7-year period. Total RNA integrity and cRNA target size distribution were assessed using the 2100 Bioanalyzer. We present Affymetrix GeneChip array performance metrics for different ocular samples processed according to a standard microarray assay workflow including several quality control checkpoints. Our review of ocular sample performance in the microarray assay demonstrates the value of considering tissue-specific characteristics in evaluating array data. Specifically, we show that Bioanalyzer electropherograms reveal highly abundant mRNAs in lacrimal gland targets that are correlated with variation in array assay performance. Our results provide useful benchmarks for other gene expression studies of ocular systems.


DNA microarrays Gene expression mRNA RNA quality Capillary electrophoresis Lacrimal gland