Evaluation of Affymetrix Gene Chip sensitivity in rat hippocampal tissue using SAGE analysis. Serial Analysis of Gene Expression.
DNA microarrays are a powerful tool for monitoring thousands of transcript levels simultaneously. However, the use of DNA microarrays in studying the central nervous system faces several challenges. These include the detection of low-abundance transcripts in highly complex tissue as well as estimating relatively low-magnitude changes in transcript levels in response to experimental manipulation. Many transcripts important to brain function have low expression levels or are expressed in relatively few cells, making them difficult to detect in the complex background of brain tissue. The aim of the present study is to evaluate the sensitivity of Gene Chip detection of transcripts in brain by using results from serial analysis of gene expression (SAGE) studies. The results of this comparison indicate that Affymetrix Gene Chips, like SAGE, only reliably detect medium- to high-abundance transcripts and that detection of low-abundance transcripts, many of which have great relevance to biological function in brain, is inconsistent. Specifically, we estimate that Gene Chips reliably detect no more than 30% of the hippocampal transcriptome when using a gross hippocampal dissection as the source tissue. This report provides the first broad evaluation of Affymetrix Gene Chip sensitivity relevant to studying the brain.
Evans
Simon J
SJ
Mental Health Research Institute, 205 Zina Pitcher Place, University of Michigan, Ann Arbor, MI 48109-0720, USA. evanssj@umich.edu
Datson
Nicole A
NA
Kabbaj
Mohamed
M
Thompson
Robert C
RC
Vreugdenhil
Erno
E
De Kloet
E Ronald
ER
Watson
Stanley J
SJ
Akil
Huda
H
D000818:Animals; D006624:Hippocampus / Q000378:metabolism*; D009419:Nerve Tissue Proteins / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D018075:RNA, Complementary / Q000032:analysis* / Q000235:genetics; D051381:Rats; D017207:Rats, Sprague-Dawley; D015203:Reproducibility of Results; D014158:Transcription, Genetic / Q000235:genetics*
D009419:Nerve Tissue Proteins; D018075:RNA, Complementary