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.

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

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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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Project description:The antisense insertion of a canine short interspersed element (SINEC_Cf) in the pigmentation gene PMEL (or SILV) causes a coat pattern phenotype in dogs termed merle. Merle is a semi-dominant trait characterized by patches of full pigmentation on a diluted background. The oligo(dT) tract of the Merle retrotransposon is long and uninterrupted and is prone to dramatic truncation. Phenotypically wild-type individuals carrying shorter oligo(dT) lengths of the Merle allele have been previously described and termed cryptic merles. Two additional coat patterns, dilute merle (uniform, steely-grey coat) and harlequin merle (white background with black patches), also appear in breeds segregating the Merle allele.Sequencing of all PMEL exons in a dilute and a harlequin merle reveals that variation exists solely within the oligo(dT) tract of the SINEC_Cf insertion. In fragment analyses from 259 dogs heterozygous for Merle, we observed a spectrum of oligo(dT) lengths spanning 25 to 105 base pairs (bp), with ranges that correspond to the four varieties of the merle phenotype: cryptic (25-55 bp), dilute (66-74 bp), standard (78-86 bp), and harlequin (81-105 bp). Somatic contractions of the oligo(dT) were observed in 43% of standard and 51% of harlequin merle dogs. A small proportion (4.6%) of the study cohort inherited de novo contractions or expansions of the Merle allele that resulted in dilute or harlequin coat patterns, respectively.The phenotypic consequence of the Merle SINE insertion directly depends upon oligo(dT) length. In transcription, we propose that the use of an alternative splice site increases with oligo(dT) length, resulting in insufficient PMEL and a pigment dilution spectrum, from dark grey to complete hypopigmentation. We further propose that during replication, contractions and expansions increase in frequency with oligo(dT) length, causing coat variegation (somatic events in melanocytes) and the spontaneous appearance of varieties of the merle phenotype (germline events).

			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