RNA QUALITY CONTROL on the BIOANALYZER
The most important factor in getting good microarray data is RNA quality. Degradation or contamination with protein or DNA can lead to poor labeling and hybridization. The CAT offers customers the chance to assess the quality of RNA samples via the Agilent 2100 Bioanalyzer. The Bioanalyzer uses a microfluidics based integrated chip to analyze RNA samples for size distribution.
All of the expression labeling protocols (Affymetrix, Illumina, and Agilent) require a post-labeling QC check of amplified and labeled cRNA or cDNA. Examples of post-labeling QC runs on the Bioanalyzer are shown below. The left-hand trace (left) shows a typical size distribution for amplified and labeled cRNA. The trace on the right (right) shows the same sample after fragmentation, ready to be hybridized to an Affymetrix 3' IVT array.
