1. Does your lab provide bisulfite conversion for methylation studies?  Bisulfite conversion is included in the pricing for all Illumina methylation projects.  For projects on other platforms, we can provide conversion for you for a fee.
  2. How should I provide my samples?  
    1. For Illumina methylation studies, we will provide you with 96-well Matrix plates for your samples, once you have initiated the study process.  For more information, email Roxann Ashworth.
    2. Samples for our PCR service should be provided in 96-well PCR plates, 12-strip tubes or 1.5 ml tubes.  For more information, email Laura Kasch.
    3. Samples for Pyrosequencing should be provided in 96-well PCR plates (loaded in row order, not column order) or in 12-strip tubes.  Small numbers of samples may be provided in 1.5 ml tubes.  For more information, email us.
    4. Always label your Pyrosequencing tubes/plates with your Genesifter order tracking ID.
  3. What volume and concentration should I provide for the bisulfite conversion?
    1. For Illumina chips: Please provide 80 ul of DNA at 30-50ng/ul in 1xTE (10mM Tris, 1mM EDTA, pH 8) or water.
    2. For Pyrosequencing: Please provide a minimum of 100ng per assay (amplicon).
  4. I am doing Pyrosequencing.  Which PCR & Bisulfite Conversion 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.
  5. I converted my own DNA, but I am having you do the Pyrosequencing PCR reactions.  How much DNA should I provide?  Please provide 40ng at 5ng/ul to 10 ng/ul of bisulfite converted DNA per amplicon (assay).
  6. How do I order Pyrosequencing assays?  Qiagen has over 30,000 predesigned human and rodent assays.  Please search Geneglobe for your gene of interest.  Once you select your assays, place them in a shopping cart and transfer the cart to customorders@jhmi.edu.  We will place the order for you.  By ordering through us, you receive a discounted price and free shipping.
  7. Do you offer Pyrosequencing assay design services?  If you are doing your Pyrosequencing in our facility, we will assist you with assay design.  Email us to discuss your project.
  8. I ordered my own Pyrosequencing primers.  What concentration should I bring the sequencing primer at?  DO NOT resuspend the sequencing primer.  The instrument requires that the primer be suspended in a special buffer.  Please bring us the lyophilized primer and any paperwork you received from the manufacturer.
  9. What data do I receive?
    1. Illumina methylation customers receive: Methylation GenomeStudio and profile data, minfi analysis, summary reports and README files to describe the data in each directory.
    2. Pyrosequencing customers receive a .csv file of the percent methylation values for all CpGs in their assay and a .pdf with a visual representation of the data.
  10. Do you offer services to external customers?  Yes.  Please email Roxann Ashworth to discuss your project.