We are in process of moving this FAQ to a new Seqcore Wiki
Which will contain information on Standard Sequencing as well as our many new services.


Frequently Asked Questions

This page tells everything you need to know to use the U-M DNA Sequencing Core.

Or you can search the
SeqCore site:

There's also A Brief Introduction to U of M's DNA Sequencing Core, if you want the short version of basic information about this Core.


The University of Michigan's DNA Sequencing Core provides U-M investigators access to automated DNA sequencing technology on a recharge basis. The Core processes samples on three ABI Model 3730XL sequencers. Samples are typically processed in 2 business days, and yield 800-900 nucleotides of high-quality DNA sequence data (better than 99% accuracy typically; see documents below). The cost for this service is $3.00 per sample (one template, one primer), with various discounts available for larger numbers of samples and for members of certain Centers.

The Most Frequently-Asked FAQs: Cost Template Concentration Turnaround Chromatogram Interpretation Troubleshooting

Basic Information:

  1. Intro to the UM DNA Sequencing Core
  2. What is DNA Sequencing?
    (a general tutorial page appropriate for high school-level students)
  3. Who can submit samples to this Core?
  4. Why use automated sequencing?
  5. Thinking about buying your own sequencer? Read this first!
  6. Does the Core do Genotyping as well?
  7. What types of templates can the Sequencing Core process?
  8. What will it cost?
  9. What will I get for my money?
  10. What if my DNA is longer than your machines can read?
  11. Does the Core perform Shotgun sequencing?
  12. What is the Core's privacy policy?
  13. What QA/QC measures does the Core implement to minimize mistakes?

Some global issues about our operations:

  1. There's too much to read here! What's the MINIMUM I need to know?
  2. How do I sign up?
  3. Prospective Clients From Outside the University of Michigan: Read This!
  4. What are the PI's responsibilities?
  5. How does the PI perform those tasks?
  6. How do I change the Lab Password ('PI Password')?
  7. I've forgotten the lab password! What do I do?
  8. How do I change our account numbers?
  9. How do I add (or remove) lab members?
  10. We haven't used the Sequencing Core in a long time. What do we do?
  11. What's this 'IBC' checkbox (or 'BRRC' checkbox) we have to click?
  12. Can I get discounted sequencing based on Center memberships?
  13. What if I have multiple Center memberships?
  14. Can I get bulk discounts for large-scale projects?

How to prepare samples for sequencing:

  1. How to prepare DNA.
  2. Why can't I use a spectrophotometer to measure my mini-prep DNA?
  3. Can I directly sequence a PCR product?
  4. Can I get sequence from large-insert clones like BACs?
  5. Can I get sequence directly from bacterial genomic DNA?
  6. What primers does the Core provide?
  7. How do I design my own primers?
  8. The correct concentration and volume for your template(s) and primer(s).

Submitting your samples:

  1. How do I log my samples into the Core computer? (How do I get a sample number?)
  2. Can I Get Rush Processing?
  3. What kind of tubes should I use?
  4. Can I submit my samples in 96-well plates?
  5. How do I label my samples?
  6. Why won't the computer let me submit any samples?
  7. My Login has been disabled due to an email problem! Why, and what should I do?
  8. What's this 'IBC' (or 'BRRC') thing your computer says we haven't done?
  9. Where and when can I drop off my samples for the Core?
  10. EXTERNAL CLIENTS: Where and how to mail samples.

After you've submitted samples:

  1. I made a mistake entering my sample! How can I correct it?
  2. How long will it take?
  3. Can I Get Rush Processing?
  4. How do I check the status of samples I have submitted?
  5. How will I get my results back?
  6. My sample is listed as 'done', but I can't find the data!
  7. How do I contact the Core personnel?

About your results:

  1. How will I get my sequence back?
  2. How do I get my chromatogram file?
  3. I've forgotten my password! How can I get it back so I can retrieve my data?
  4. Can't I get a hard-copy printout of my chromatogram file?
  5. I downloaded my chromatogram file. Now, how do I open it?
  6. My files are missing from the Download Server! Why???
  7. How long are files kept on the data download server?
  8. How do I interpret the results?
  9. I need some old sequence data from [1996/2003/whenever]. How do I get it?

In Case of Problems:

  1. Why won't the computer let me submit samples?!
  2. My Login has been disabled due to an email problem! Why, and what should I do?
  3. The Results email I received cuts off partway through the message! What should I do?
  4. My files are missing from the Download Server! Why???
  5. Why is my text sequence slightly different than my chromatogram's sequence?
  6. What do I do in case of problems?
  7. My primer works fine for PCR - why can't you sequence with it?
  8. My samples produced only blank lanes. Why?
  9. The technicians reported 'poor resolution' for my samples. Why?
  10. Sequencing worked - sort of - the data aren't very good. Why?
  11. What are the most common reasons for a sequencing reaction to fail?
  12. I think the Core may have made a mistake with my samples.
  13. How do I contact the Core personnel?

Regarding the subsequent billing:

  1. How will these services be billed?
  2. How can I make sure we're paying the right amount?
  3. What tools does the PI have for managing expenditures?
  4. How can the Departmental Financial Contacts resolve accounts?

Other Core Directors frequently inquire about our excellent data system.

If you would like to learn more about it, click here.


For comments or suggestions, please contact Robert H. Lyons (boblyons@umich.edu)
Last updated 9-Jan-04