Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Serum Starvation/Refeeding RNA vs. RAP

ABSTRACT: Low abundance mRNAs are more difficult to examine using microarrays than high abundance mRNAs due to the effect of concentration on hybridization kinetics, signal-to-noise ratios, and interference between signals from mRNA isoforms. Individual sequences in LCRs are more highly represented than in the mRNA population 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, as serum-starved fibroblasts responded to the reintroduction of serum. Thus, this target preparation strategy considerably increases the sensitivity of spotted cDNA microarrays.

ORGANISM(S): Homo sapiens

SUBMITTER: Yipeng Wang

PROVIDER: E-GEOD-2655 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Enhanced microarray performance using low complexity representations of the transcriptome.

Rondeau Gaëlle G McClelland Michael M Nguyen Toan T Risques Rosana R Wang Yipeng Y Judex Martin M Cho Ann H AH Welsh John J

Nucleic acids research 20050624 11

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 abu ...[more]

PMID: 15987785

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Dataset Information

Serum Starvation/Refeeding RNA vs. RAP

Publications

Enhanced microarray performance using low complexity representations of the transcriptome.

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