Transcriptomics,Multiomics

Dataset Information

3

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.

OTHER RELATED OMICS DATASETS IN: PRJNA92121

SUBMITTER: Yipeng Wang   Gaelle Rondeau 

PROVIDER: E-GEOD-2655 | ArrayExpress | 2010-06-10

SECONDARY ACCESSION(S): GSE2655PRJNA92121

REPOSITORIES: GEO, ArrayExpress

Dataset's files

Source:
Action DRS
E-GEOD-2655.README.txt Txt
E-GEOD-2655.idf.txt Idf
E-GEOD-2655.processed.1.zip Processed
E-GEOD-2655.sdrf.txt Txt
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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]

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