1. Does your lab provide bisulfite conversion for methylation studies?  Bisulfite conversion is included in the pricing for all 450K projects of more than one plate.  For projects on other platforms, we can provide conversion for you for a fee.
  2. I only have one plate for 450K analysis and want to do my own conversion.  Which kit should I use? Illumina recommends the following kits for bisulfite conversion.
    1. EZ DNA Methylation Kit for 50 DNA reactions (supplied with capped columns) (Zymo Research, catalog # D5001)
    2. EZ DNA Methylation Kit for 200 DNA reactions (supplied with capped columns) (Zymo Research, catalog # D5002)
    3. EZ-96 DNA Methylation Kit for 2×96 DNA conversion reactions (deep-well Zymo-Spin I-96 Filter Plate) (Zymo Research, catalog # D5004)
    4. Note: Bisulfited DNA is single stranded and unstable, so please be sure to arrange a slot in the SNP Center lab with your project manager before beginning the process.
  3. I am doing Pyrosequencing.  Which kit should I use?  You may use any kit.  If you use Qiagen reagents for everything in your assay (i.e. off the shelf methylation assay, bisulfite conversion and PCR reagents), the assays are guaranteed and Qiagen will replace failing assays.
  4. What volume and concentration should I provide for the bisulfite conversion?