Characterization of the effect of sample quality on high density oligonucleotide microarray data using progressively degraded rat liver RNA.

ABSTRACT:

Background

The interpretability of microarray data can be affected by sample quality. To systematically explore how RNA quality affects microarray assay performance, a set of rat liver RNA samples with a progressive change in RNA integrity was generated by thawing frozen tissue or by ex vivo incubation of fresh tissue over a time course.

Results

Incubation of tissue at 37 degrees C for several hours had little effect on RNA integrity, but did induce changes in the transcript levels of stress response genes and immune cell markers. In contrast, thawing of tissue led to a rapid loss of RNA integrity. Probe sets identified as most sensitive to RNA degradation tended to be located more than 1000 nucleotides upstream of their transcription termini, similar to the positioning of c

SUBMITTER: Thompson KL 

PROVIDER: S-EPMC2082023 | biostudies-literature | 2007 Sep

REPOSITORIES: biostudies-literature