Quality Control

Quantification of Concentration and Quality Assessment of samples are the most critical steps for a successful microarray analysis. RNA should be high quality with good 18S and 28S peaks. Genomic DNA should be high molecular weight. The Core routinely performs the following QC metrics:

Quantification of RNA/DNA by Spectrophotometer:

RNA/DNA yield is quantified by UV absorption (NanoDrop ND-1000 Spectrophotometer) (1 AU 260 equals 40 ug/ml for RNA, 50 µg/ml for DNA). Purity is estimated by the 260 and 280 nm absorbance ratio. Acceptable values are between 1.7 and 2.1.

Quality Assessment by Agilent 2100 Bioanalyzer:

The quality of sample RNA is assessed using RNA 6000 Labchip Kit on the Agilent 2100 Bioanalyzer. The Bioanalyzer determines the integrity/purity of the RNA samples and permits the screening of total and mRNA sample degradation and ribosomal RNA contamination.

Up to twelve samples may be loaded per disposable RNA Labchip. A RNA 6000 ladder is also loaded on a specified well and is used as a reference for data analysis and a built-in quality control measure. The run takes approximately 25 minutes during which the samples are sequentially separated on the chip through a single separation channel. After each separation the quality and integrity of RNA can be determined through visual inspection of each electropherogram.

The following Electropherograms (Run on 2100 Bioanalyzer and produced by Agilent Technologies) depict the differences between High Quality vs. Degraded RNA.


This QC step is repeated following the labeling procedure to ensure the probes are efficiently labeled and have the correct size before hybridization to the chips.