It’s very important that users provide us DNA or RNA samples at required quality and quantity. Please refer to the Services section for specific requirements of sample submission. Here are some general guidelines for sample preparation and quality control:

Total RNA preparation

• Total RNA samples for microarray analysis should be free of proteins, DNA, phenol, ethanol, and salt.
• We recommend RNeasy mini kit from Qiagen for RNA preparation
• If TRIzol is used to extract RNA from tissues, we recommend a cleanup procedure with Qiagen RNeasy mini kit following the phenol extraction.

RNA quantitation
We recommend the NanoDrop spectrophotomer for quick and accurate quantitation. NanoDrop at our center is available to you free of charge.

RNA quality assessment
The quality of total RNA samples is the most important factor in microarray experiments. When you provide us total RNA samples for labeling, we always perform RNA integrity check by running RNA samples on Agilent 2100 Bioanalyzer. If there is significant degradation (when RNA Integrality Number, or RIN, is below 8.0), we will NOT perform sample labeling. Instead, we will request users re-submit total RNA samples.

If you perform sample labeling yourself, we highly recommend that you also perform RNA integrity analysis first.

Genomic DNA Preparation for SNP and microsatellite 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 be also amplified and affect the data.
• For Affymetrix SNP arrays, DNA samples should be in reduced EDTA TE buffer (10 mM Tris, 0.1 mM EDTA, pH 8.0); for Illumina SNP arrays, DNA samples can be in regular TE buffer (10 mM Tris, 1 mM EDTA, pH 8.0)
• QIAamp Kit from Qiagen has been used successfully for DNA preparation

DNA quantitation
We recommend the NanoDrop spectrophotomer for quick and accurate quantitation. NanoDrop at our center is available to you free of charge.

Genomic DNA Quality Assessment:

• DNA samples must not be highly degraded. We recommend quality check on 1% agarose gel. High quality genomic DNA should give a major band at 10-20 kb on the gel.
• We also recommend that users perform a regular PCR amplification on the genomic DNA samples with a pair of primers of users' choice. This is to ensure that genomic DNA samples are free of PCR inhibitors.