An Introduction to the DNA Sequencing Core
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The DNA Sequencing Core
provides University of Michigan investigators access to high-quality automated
DNA Sequencing technology on a recharge basis. The cost
of this service
compares favorably with similar cores at other institutions, as does
the quality of the data obtained. Turnaround time is
results are usually returned by email within 48 hours of
sample submission. This document provides basic information needed by
prospective clients of the Core.
Last updated 23-Jul-07
Description of Service
The Core accepts DNA samples
(pure plasmids, mini-prep plasmids, M13
clones, cosmids, lambda clones, PCR products, gel isolated fragments, bacterial genomic)
and processes them
according to protocols for Applied Biosystems DNA Sequencers (Model 3730 XL sequencer).
One sequencing run (one template, one primer) typically produces 900
nucleotides of high-quality sequence data or more, for good-quality template and a well-designed
primer. The results are returned in two forms: a raw sequence file and a chromatogram file.
The sequence file (a flat ASCII text file) is returned to the researcher by electronic mail.
The chromatogram file is available on our data server (password protected to prevent unauthorized
distribution of your data).
Standard Primers Provided
The Core provides five standard primers free of charge: T7, T3, SP6, M13FORW and M13REV.
Please see the table of primers and their
sequence for reference. We will also sequence using custom primers submitted by
the individual investigators. See Design of Primers
for Automated Sequencing for suggestions on how to design your own primers.
Each sequencing gel includes at least one lane of standard DNA known to generate good
sequence. In addition, if any of the customers' samples utilize one of the Core's five
standard primers, we will also include a positive control lane for that primer. The
gel, sample handling and data analysis are extremely reliable and the Core personnel
have a very low rate of error. If any problems are indicated in our sample processing,
we repeat the affected samples free of charge.
We typically process samples within two business days after
receipt. Check the current backlog for up-to-date
Samples are processed Monday through Friday for overnight instrument
runs. Processing typically begins between 6:00 and 10:00 on that day's reactions, and
the gels are loaded into the sequencers for their overnight run at about 4:00 PM. The
data are processed the following day and returned by email to the customers, usually between
11:00 AM and 4:00 PM.
Some additional notes:
- If the current backlog is more than 2 business days,
you may wish to consider requesting Rush Processing
- If we have no backlog, you may get the faster
turnaround time by
bringing the samples to the core before 9:00 AM so they may be selected
for that day's processing. We cannot guarantee this, however,
unless you request RUSH service.
- In the event the numbers of samples exceeds our ability to process them, on-campus
investigators take precedence over off-campus
clients, and bulk-rate samples (96-well plates) take lower priority
than normal samples.
The basic cost of DNA sequencing is
$3.00 for processing one template
with one primer for all clients affiliated with the University of Michigan.
Non-University clients are accommodated as time
permits. Clients who submit entire 96-well plates of samples are eligible
for a discount ( final price of $2.40 per lane).
Discounts are also
offered to affiliates of certain research units or of specific center grants. Please
consult with the PI of your center grant to see if you are eligible for such a
discount. The best discounts can be obtained via high-volume
submission. Contact the Core Director for more
| When your samples have been completed, you will receive an email with
the DNA sequence of your sample. This is what's known as a "flat ASCII file", and can be
transferred into most standard DNA sequence analysis programs by cut/paste or other
We also make the actual chromatogram available for you.
Certain sequence assembly packages will import these files, allowing you to make
critical judgements on sequence quality while you are assembling the final sequence - this
is highly recommended.
The chromatograms are available on the Download Server.
You will need your PI's Login and password
Chromatograms are available for downlowad for 2 weeks, after which
the data is archived.
We also provide links to several
programs capable of opening and viewing
The sequence returned to investigators may be up to
1100 nucleotides long, but in general only some of that is reliable. The amount depends
on a variety of factors, but the primary
determinant is the quality of the template DNA.
Beyond that high-quality sequence, the remainder of the file is useful in specific
experiments where sequence accuracy is unimportant.
It is crucial for each customer to evaluate their own data and to
determine the extent of
reliable data. Because data evaluation is highly dependent on your
individual needs, we
cannot perform this step for you. See our page on
Interpretation of Sequencing Chromatograms if you are unsure how to
evaluate the results.
Automated sequencing is very reliable in the hands of our experienced
technicians. As a precaution, we always check that control samples
sequenced properly, that excess terminators were removed, that the gel
resolution was adequate and that the computerized data extraction
proceeded normally. If a problem is detected in any of these, customer
samples are repeated free of charge.
Extensive information is available on our web site to help you design
effective sequencing experiments, and to aid you in troubleshooting the results of your
sequencing. Please see our Frequently
Asked Questions page for more information on these topics.
The Core has no control over the quality of template,
the design of the
primer or the presence of 'problem' spots on the template. We will do
our best to help you to avoid such problems, but we must charge for
sequencing reactions that fail for such reasons.
The Core Location and Hours of Operation are
posted online and e-mailed to you when you submit samples.
Please feel free to call the Core Director,
Dr. Robert Lyons, at 764-8531.
For general problems, including using the website and checking your samples you can contact
DNA Sequencing Core Main Office at 764-1461.
We also have an LSI Submission Desk which
can be reached at 765-9168
You can contact the DNA Sequencing Core Lab at 764-8067, but remember, technicians
are kept very busy processing samples, most issues can best be handled by contacting
the office or the Core Director
Back to Sequencing Core Home Page
Please address any comment, questions, or suggestions to
Robert H. Lyons(firstname.lastname@example.org)