Microarray Sample Submission

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 and Submission for Illumina Infinium BeadArray-based Genotyping and Mapping

1. Suspend DNA samples in either water, Tris (Qiagen EB is fine) or low TE (0.1 mM EDTA). Higher concentrations of EDTA (as in TE) could be inhibitory to some enzymatic steps in the process.

2. Mix the samples WELL (It is ok to vortex for the purpose of the mapping arrays. Do not vortex if the same sample will be used for other applications).

3. Quantify samples in duplicate using a spectrophotometer (e.g. Nanodrop) or fluorometer (e.g. Qubit). All samples should be in the range of 50-100 ng/ul.

  • Samples under 50 ng/ul need to be concentrated.
  • Please dilute samples with DNAse free water if the concentration is above 100 ng/ul. (We recommend aiming for 80 ng/ul).
  • The IIHG Genomics Division has a NanoDrop spectrophotometer available for use to measure concentrations. We will guide you on how to use it. Print out both the results table and the profiles of the samples.

4. Run all samples on a ~1% agarose gel including a MW ladder (e.g., 1 kb-plus ladder). Load 3 ul of sample and 6 ul of ladder. You want to see a high molecular weight band of approximately the same brightness for all the samples.

5. Please talk to us about sample volume and arrangement on the submission plate. We usually request 20 ul of each sample, however, there are exceptions. Also, the various microarray sample prep workflows start with different configurations of the samples on the plate.

6. Please provide the Nanodrop results (table and profiles) and the gel image along with your samples.

 

DNA Sample Preparation and Submission for Illumina Infinium Methylation Epic Arrays

1. Suspend DNA samples in either water, Tris (Qiagen EB is fine) or Low TE (0.1 mM EDTA).  Higher concentrations of EDTA (as in TE) could be inhibitory to some enzymatic steps in the process.

2. Mix the samples WELL, but avoid aggressive vortexing that might shear the DNA.

3. Quantify samples using both a spectrophotometer (e.g., NanoDrop) and fluorometer (e.g., Qubit).  All samples should be in the range of 15-20 ng/ul, as measured by QUBIT HS assay. 

  • Please dilute samples with DNase-free water if the concentration is above 20 ng/ul, then confirm the final concentration with the QUBIT.
  • The IIHG Genomics Division has both a NanoDrop and Qubit available to measure concentrations. We will guide you on how to use them.

 4. Run all samples on a ~1% agarose gel, including a MW ladder (e.g., 1 kb+ ladder). Load 150-200 ng of DNA and 6 ul of ladder.  You want to see a high molecular weight band of approximately the same brightness for all samples.

5. Before plating, we would like to see the NanoDrop results (table and profiles), the final Qubit results and the gel images.  It is difficult to make substitutions once the samples are plated.

6. Please talk to us about sample volume and arrangement on the submission plate.   We request 45 ul of each sample @15-20 ng/ul, plated in columns (not rows).


Contact Information

116 EMRB

Phone: (319) 335-7928