FAQ

DNA sequencing core facility has moved to the VA Medical Center. For your convenience, we have reserved a freezer in the Medical Science Building and an Order Form drop box to receive your samples. You can also bring your samples directly to our facility at the VA, room D-3013.

4. HOW DO I GET MY RESULTS?

You will be notified by e-mail when electronic files have been transferred into your web folder. In addition, the hard copies are placed in separate file folders with your PIs’ name on them. These hard copies can be picked up at MS, Room 4008. For our clients outside IUPUI campus, we usually send data by email. We can also send your data on disks or CD for an additional charge.

5. WHAT TYPES OF TEMPLATES CAN THE SEQUENCING CORE PROCESS?

DNA Sequencing Core Facility accepts the following samples for sequencing:

Single-Stranded DNA

Double-Stranded DNA

PCR products

DNA fragments

Large DNA such as Plasmids over 20kb, Lambda, Cosmids, and BACs

(Please contact Core personnel for further detail before submitting Large DNA for sequencing).

HOWEVER,

a. We accept only prepared DNA samples, not unpurified or tissue samples

b. The investigator is expected to interpret the results, assemble the sequence and design any needed primers

c. We do not perform paternity testing. However, we have a ABI 377 DNA Sequencer that can be used for this purpose. Please contact core personnel for further details.

6. HOW DO I SUBMIT MY SAMPLES?

Our Core service is trying hard to make our turn around time faster. Your cooperation is critical in helping us minimize our turn around time. The following are some recommendations when submitting for your samples for sequencing:

Your submitted Order Form must clearly indicate PI’s name, contact person, and account number.

DNA and primers should be submitted at the required concentration

DNA samples and primers should be in different eppendorf tubes and clearly labeled (we prefer that you don’t mix DNA and primer in a tube).

Your samples must be in the holding container with the name labeled the same as the contact person’s name indicated in the Order Form.

11. CAN YOU HANDLE LARGE SCALE SEQUENCING PROJECTS?

Our Core Facility operate two ABI sequencers, the 3100 Genetic Analyzer, and the 377 DNA sequencer. We routinely use the 3100 Genetic Analyzer. The 377 DNA sequencer is available for back up. We have the capacity to perform about 500 samples per week. We are happy to discuss and schedule for your need if you have large scale sequencing projects. Please contact us at (317) 274-5044 or e-mail us at okheav@iupui.edu.

12. HOW LONG DOES IT TAKE TO GET MY RESULTS?

DNA sequencing is a one business day service starting from the samples are received.

13. HOW DO I OPEN MY ELECTRONIC FILES?

There two types of files in your web-folder:

A text file (.seq) with the base sequence. This file can be opened in word format.

An ABI file (.abi) contains the nucleotide sequence, electropherogram, and other information about the run conditions. This file requires the Chromas software to view it. You can download Chromas from this website.

14. WHAT IF I WANT TO REUSE A DNA OR PRIMER SAMPLE THAT HAS BEEN USED IN DNA SEQUENCING AT YOUR FACILITY IN THE PAST?

Our space is limited. DNA samples and primers are kept for two weeks starting from the date they are received. If requested with the indication on the Order Form to keep DNA samples and primers for the near future use, we will keep for up to two weeks.

16. WILL YOU CHARGE FOR FAILED SEQUENCE?

This is a very challenging question. Our Sequencing Core is fully committed to serving your need. We try the best we can to keep the Core running and to make you happy. In the past we did not charge for failed sample and we experienced repeating the same old sample and it failed many times. To avoid this problem we will charge for failed sample BUT we are happy to discuss the problems and repeat this failed sample free of charge one time. It is critical, however, that all samples meet criteria stated on order form.

17. I THINK THE CORE MADE A MISTAKE WITH MY SAMPLES.

If the error was ours, we'll certainly do whatever we can to correct the situation. We'd be glad to repeat the sample to find out if there was a mix-up as follow:

We will resequence the original sample in its original tube.

If the repeated sequencing works, you will not be charged for the repeat.

If your sample fails a second time, we will charge you the original run and the repeat as well.

18. CAN I GET MY OLD SEQUENCE DATA FROM 2 YEARS AGO?

We recommend that you save you files into your computer or disks. Our web-folder sever has a limited capacity. We normally keep new sequencing files in our sever for about half a year from the date they were run. Old sequencing files are deleted to provide space for the new run files. We are working to obtain a longer storage database.

19. CAN I HAVE A WEB-FOLDER? WHAT ARE THE REQUIREMENTS?

IUPUI researchers are encouraged to have web-folders for receiving sequencing data. It is the easy way to view and edit your results. The process to have a web-folder is as follow:

a. If you are the PI, we need your iupui email user name. You will have full access in your folder.
b. If your are working in an IUPUI laboratory, we also need your iupui email user name and permission from your PI before we can give you access or create a sub. folder inside your PI’s folder.
c. Give us a call at (317) 274-5044 to set up your folder with the folder’s name you prefer.

20. SOME COMMON REASONS WHY SEQUENCING FAILS...

a. Inadequate template concentration (the most common reason)

b. Bad 260/280 ratio indicating RNA present

c. Salt contamination in sample

d. Mis-paired primers

e. Multiple priming sites present

f. Primer dimmers

g. Primer Tm too low

h. Secondary structure

i. Sequencing incorrect PCR products

j. Calculation error in primer concentration

k. Overloading of miniprep purification kits

l. Mixed-up samples and primers