Transcription profiling of Stratagene univeral human reference RNA using different amounts of RNA to investigate array variability

ABSTRACT: Affymetrix U133 Plus 2.0 arrays were hybridized with varying amounts of starting material to determine whether different measurements of gene expression were observed. Experiment Overall Design: 1 ug, 2, ug, 5, and 10 ug of Stratagene universal human reference RNA was used to setup a series of reactions which were subsequently hybridized to Affymetrix U133 Plus 2.0 arrays. 1 ug samples were performed in triplicate and the entire experiement was repeated. BACKGROUND: There are many potential sources of variability in a microarray experiment. Variation can arise from many aspects of the collection and processing of samples for gene expression analysis. Oligonucleotide-based arrays are thought to minimize one source of variability as identical oligonucleotides are expected to recognize the same transcripts during hybridization. RESULTS: We demonstrate that although the probes on the U133A GeneChip arrays are identical in sequence to probes designed for the U133 Plus 2.0 arrays the values obtained from an experimental hybridization can be quite different. Nearly half of the probesets in common between the two array types can produce slightly different values from the same sample. Nearly 70% of the individual probes in these probesets produced array specific differences. CONCLUSION: The context of the probe may also contribute some bias to the final measured value of gene expression. At a minimum, this should add an extra level of caution when considering the direct comparison of experiments performed in two microarray formats. More importantly, this suggests that it may not be possible to know which value is the most accurate representation of a biological sample when comparing two formats.

ORGANISM(S): Homo sapiens

SUBMITTER: Sean Yoder 

PROVIDER: E-GEOD-3062 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress