Enhanced microarray performance using low complexity representations of the transcriptome.
Low abundance mRNAs are more difficult to examine using microarrays than high abundance mRNAs due to the effect of concentration on hybridization kinetics and signal-to-noise ratios. This report describes the use of low complexity representations (LCRs) of mRNA as the targets for cDNA microarrays. Individual sequences in LCRs are more highly represented than in the mRNA populations from which they are derived, leading to favorable hybridization kinetics. LCR targets permit the measurement of abundance changes that are difficult to measure using oligo(dT) priming for target synthesis. An oligo(dT)-primed target and three LCRs detect twice as many differentially regulated genes as could be detected by the oligo(dT)-primed target alone, in an experiment in which serum-starved fibroblasts responded to the reintroduction of serum. Thus, this target preparation strategy considerably increases the sensitivity of cDNA microarrays.
Sidney Kimmel Cancer Center 10835 Altman Row, San Diego, CA 92121, USA.
Gaëlle
G
Rondeau
Michael
M
McClelland
Toan
T
Nguyen
Rosana
R
Risques
Yipeng
Y
Wang
Martin
M
Judex
Ann H
AH
Cho
John
J
Welsh
D002460:Cell Line; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D006801:Humans; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012333:RNA, Messenger / Q000032:analysis* / Q000737:chemistry / Q000378:metabolism; D014158:Transcription, Genetic
D009838:Oligodeoxyribonucleotides; D012333:RNA, Messenger; C027903:oligo (dT)