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

Christina A. Harrington, Winther Michael Winther, M. Garred Michelle

Research output: Contribution to journalReview articlepeer-review

8 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)243-249
Number of pages7
JournalJournal of Ocular Biology, Diseases, and Informatics
Volume2
Issue number4
DOIs
StatePublished - Dec 2009

Keywords

  • Capillary electrophoresis
  • DNA microarrays
  • Gene expression
  • Lacrimal gland
  • MRNA
  • RNA quality

ASJC Scopus subject areas

  • Ophthalmology
  • Genetics

Fingerprint

Dive into the research topics of 'Use of bioanalyzer electropherograms for quality control and target evaluation in microarray expression profiling studies of ocular tissues'. Together they form a unique fingerprint.

Cite this