Please consult with the IIHG Genomics Division microarray personnel before starting a SNP Genotyping, Mapping or Methylation Array project. It is our experience that the most important factor in the success of an array project is the quality and correct quantity of the DNA samples. Below are our guidelines for providing samples that typically give successful array data.

DNA Sample Preparation/Submission for Illumina Infinium Bead Array-based Genotyping and Mapping

1. DNA isolation method should include an RNase-treatment/removal.  
2. Suspend DNA samples in either water, Tris Buffer (Qiagen EB[10mM Tris-Cl, pH 8.0, 1mM EDTA] is fine) or low TE (0.1 mM EDTA).  Higher concentrations of EDTA could be inhibitory to some enymatic steps in the process. 
3. Mix the samples WELL, but avoid aggressive vortexing that might shear the DNA. 
4. For final submission, quantify samples with a fluorometer (e.g. Qubit).  

All samples should be in the range of 50-80 ng/ul.  

• Start by getting samples 'into range' using the Nanodrop.  
• Dilute samples with nuclease free water if needed.  
• Confirm the final concentration with the Qubit.  For final submission, all samples should be in the range of 50-80 ng/ul, as measured by Qubit HS assay.  
• We would like a minimum 10ul of each sample.  

​The IIHG Genomics Division has both a NanoDrop and Qubit available to measure concentrations. We will guide you on how to use them. 

5. Run all samples on a ~1% agarose gel including a Mol.Wt. ladder (e.g., 1 kb plus ladder). Load 200 ng of sample and 6 ul of ladder. You want to see a high molecular weight band of approximately the same brightness intensity for all the samples.  Differing intensities may be a sign of remaining RNA and/or degredation.  
6. Before plating, we would like to see the final Qubit results and the gel images.  It is difficult to make substitutions once samples are plated.  

Please talk to us about sample volume and arrangement on the submission plate.  The various microarray sample prep workflows may start with different concentrations and different configurations of the samples on the plate.​

DNA Sample Preparation/Submission for Infinium Methylation (EPIC) Arrays

1. DNA isloation method should include RNase-treatment/removal.
2. Suspend DNA samples in either nuclease free water, Tris Buffer (qiagen EB [10 mM Tris-Cl, pH 8.0, 1 mM EDTA] is fine) or Low TE (0.1 mM EDTA).  Higher concentrations of EDTA could be inhibitory to some enzymatic steps in the process. 
3. Mix the samples WELL, but avoid aggressive vortexing that might shear the DNA.
4. For final submission, quantify samples with a fluorometer (e.g. Qubit):

• Start by getting samples 'into range' using the Nanodrop.  
• Dilute samples with nuclease free-water if needed.
• Confirm the final concentration with the Qubit.  For final submission, all samples should be in the range of 50-60 ng/ul, as measured by Qubit HS assay.  Higher concentrations have not worked well in the methyl-conversion reaction.  
• We would like 25 ul of each sample  

The IIHG Genomics Division has both a NanoDrop and Qubit available to measure concentrations. We will guide you on how to use them.

5. Run all samples on a ~1% agarose gel, including a Mol. Wt. ladder (e.g., 1 kb plus ladder). Load 200 ng of DNA and 6 ul of ladder.  You want to see a high molecular weight band of approximately the same brightness intensity for all samples.  Differing intensities may be a sign of remaining RNA and/or degredation.  
6. Before plating, we would like to see the final Qubit results and the gel images.  It is difficult to make substitutions once the samples are plated.

Please talk to us about sample volume and arrangement on the submission plate.   The various microarray sample prep workflows may start with different concentrations and different configurations of the samples on the plate.  

Contact Information

116 EMRB
Phone: (319) 335-7928