Total RNA Preparation for Expression Analysis

Total RNA samples for microarray analysis must be free of proteins, DNA, phenol, ethanol, and salts.
We recommend using the RNeasy Kit (Qiagen) or similar column-based methods for RNA preparation. If TRIzol-based extraction is used, we strongly advise performing an additional cleanup using the Qiagen RNeasy Mini Kit or similar column-based methods to remove residual contaminants.

RNA Quantification

We recommend using Qubit® fluorometric quantification, which provides accurate and sensitive measurement of RNA concentration.

RNA Quality Assessment

RNA integrity is one of the most critical factors in successful gene-expression experiments.
All submitted total RNA samples are evaluated using the Agilent 2100 Bioanalyzer.

• Samples with RIN < 7.0 are considered significantly degraded.
• In such cases, we will request the user to provide new RNA of sufficient quality.

Genomic DNA Preparation for SNP Genotyping

Genomic DNA samples must be free of PCR inhibitors (e.g., heme, high concentrations of EDTA or salts) and must not contain DNA from other sources. Contaminating DNA will be co-amplified during the universal amplification step used in SNP microarrays, compromising data quality.
Buffer requirements:

• Illumina SNP arrays: Regular TE buffer (10 mM Tris, 1 mM EDTA, pH 8.0)

DNA Quantification

We recommend Qubit® fluorometric quantification for fast and accurate measurement of DNA concentration.

Genomic DNA Quality Assessment

Genomic DNA must not be highly degraded. We recommend assessing integrity using a Bioanalyzer or a 1% agarose gel.

• High-quality genomic DNA typically appears as a major band around 10–20 kb.

As an additional quality check, users should perform a standard PCR amplification using primers of their choice to verify that the DNA is free of PCR inhibitors.