Total RNA preparation for expression analysis

Total RNA samples for microarray analysis should be free of proteins, DNA, phenol, ethanol and salt.

We recommend RNeasy kit from Qiagen or similar for RNA preparation. If TRIzol based methods are used to extract RNA from tissues, we recommend a cleanup procedure with Qiagen RNeasy mini kit following the phenol extraction.

RNA quantitation

We recommend Qubit® fluorometric quantitation.

RNA quality assessment

The quality of total RNA samples is the most important factor in microarray gene expression experiments. When you provide us total RNA samples for labelling, we always perform an RNA integrity check by running RNA samples on an Agilent 2100 Bioanalyzer. If there is significant degradation (when RNA Integrity Number, or RIN, is below 7.0), we will request the customer to re-submit total RNA samples of satisfactory quality.

Genomic DNA Preparation for SNP genotyping

Genomic DNA samples should be free of PCR inhibitors (such as heme and high concentrations of EDTA and salt).

DNA samples must not be contaminated with other sources of DNA. This is particularly important in SNP microarrays, as a universal amplification step is involved. Any contaminant DNA will also be amplified and affect the data.

For Illumina SNP arrays, DNA samples can be in regular TE buffer (10 mM Tris, 1 mM EDTA, pH 8.0), for Affymetrix SNP arrays, DNA samples should be in reduced EDTA TE buffer (10 mM Tris, 0.1 mM EDTA, pH 8.0).

DNA quantitation

We recommend the Qubit® fluorometric quantitation for quick and accurate quantitation.

Genomic DNA Quality Assessment

DNA samples must not be highly degraded. We recommend quality check on a Bioanalyzer or a 1 % agarose gel. High quality genomic DNA should give a major band of 10-20 kb on the gel.

We also recommend that users as a quality check perform a regular PCR amplification on the genomic DNA samples with a pair of primers of users' own choice. This is to ensure that genomic DNA samples are free of PCR inhibitors.