Estimating RNA-quality using GeneChip microarrays.

ABSTRACT:

Background

Microarrays are a powerful tool for transcriptome analysis. Best results are obtained using high-quality RNA samples for preparation and hybridization. Issues with RNA integrity can lead to low data quality and failure of the microarray experiment.

Results

Microarray intensity data contains information to estimate the RNA quality of the sample. We here study the interplay of the characteristics of RNA surface hybridization with the effects of partly truncated transcripts on probe intensity. The 3'/5' intensity gradient, the basis of microarray RNA quality measures, is shown to depend on the degree of competitive binding of specific and of non-specific targets to a particular probe, on the degree of saturation of the probes with bound transcripts and on the distanc

SUBMITTER: Fasold M 

PROVIDER: S-EPMC3519671 | biostudies-literature | 2012 May

REPOSITORIES: biostudies-literature