Microarray Sample Submission

DNA for Array-based Genotyping and Mapping

Please consult with the IIHG Genomics Division microarray personnel before starting a SNP Genotyping or Mapping Array project. It is our experience that the most important factor in the success of mapping or genotyping arrays is the quality and correct quantity of the DNA samples.

Below are our guidelines for providing samples that typically give successful array data.

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.

Contact Information

116 EMRB

Phone: (319) 335-7928