Data Delivery

Data are delivered to the PI’s DNA subdirectory on the OSRF FTP Data Server, but every user will need their own account to access the server and retrieve results. Users will receive an email notification to the address that they entered in the digital order request when data are available for download.

OSRF FTP Data Server:  Each user will need to email the core to request access to the Sanger sequencing results. We will facilitate your OSRF FTP Data Server account setup, if necessary, at that time. When making a request please provide the following information:

• User first and last name, CNET ID, and email address
• PI first and last name
• Do you have an account linked to another OSRF core?

Failure to establish your OSRF Data Server account or request access to sequencing results prior to submitting orders will cause delays in results delivery.

Web Browser

You may use a web browser to access the OSRF FTP Data Server: https://coresdl.uchicago.edu/Login/. You will receive account set up instructions from the data server administrator: jmecyssine@uchicago.edu.

To meet UChicago security policies:

1. Each user will be assigned there own account to access the server.
2. User accounts will require 2-factor authentication.
3. Password sharing among lab members is not permitted.

FTP transfer in a web browser

A web browser can be used to transfer individual files using SFTP by connecting to this address: https://coresdl.uchicago.edu. Provide your username and password that were provided during account setup to connect. 

FTP transfer by client program

On Windows, Macs and Unix you can use FTP client software such as Filezilla (download from here). Connect and login using “coresdl.uchicago.edu” as the host address, and then your username and password. You will be able to transfer individual files, multiple selected files, or whole folders, usually by dragging them from one window pane to another.

Data expiration 

We maintain files on our servers for approximately six months, depending on demand. Please download your sequence files to your own machines to work on them, as files will be purged from the server periodically. We also ask that you disconnect from the server as soon as possible to prevent saturation of our server connections.

Additional help

You can reset your password via the Forgot Password link at: https://coresdl.uchicago.edu/Login/. Please use this option if you are locked out because your password may have expired. 

If you encounter problems connecting to the OSRF FTP Data Server then please email osrfhelp@osrfmailsrv.uchicago.edu. This is the most efficient method to resolve issues, because our core does not administrate the server.

DNA template quality

The most common cause of the failed sequencing reactions is low concentration template. First confirm that your samples meet the concentration guidelines suggested on our website. Another common problem is sample contamination by PCR inhibitors (e.g.: ethanol, salts, EDTA among others) that can reduce or totally inhibit the efficiency of our cycle sequencing reactions. You can use a nanodrop to evaluate the concentrations and to some extent the quality via the 260/280 and 260/230 ratios.

Primer failure

If those values do not indicate any obvious issues then it’s possible that primer failure is the problem. If this is a plasmid or new insert, consider submitting a small sequencing order with your preferred sequencing primer and another primer that has a binding site on the plasmid (ideally a core-supplied primer). Alternatively, you can run a PCR reaction with your preferred primer and another with a binding site on the plasmid to test your primer. Be sure to run the products out on an agarose gel to confirm the reaction produced the expected amplicon size.

Beginning and end of sequence

The quality of Sanger sequence reads is low in the first 20 to 40 bases and also diminishes with read length. The data in the first 20 – 40 bases and past 800 are generally unreliable, but you should review your data to confirm that the quality meets your needs for your specific application. To do so you’ll need to review the chromatogram via the ab1 file to determine where the quality becomes reliable in your sequences or use software that interprets the individual base quality scores to automatically trim the sequences.

Our quality review

We run a positive and negative sequencing control on every sequencing plate. We perform a data quality check of these control prior to delivering sequencing data. Following our submission guidelines ensures that we have enough sample on primer on hand to resequence your reactions if we detect that technical errors on our end have contributed to poor data quality.

Resequencing policy 

Request

We are always happy to resequence reactions upon client request. Please reply to the data delivery notification email that you receive to request resequencing or further data review.

Supply

We will only resequence reactions from the original order that you submitted to us. If we do not have sufficient volumes on hand then you will need to submit a new order.

Cost

We only charge for resequencing if the results are consistent with the original data that we produced.

• Software from Applied Biosystems for viewing and editing chromatograms, among other application may be found here.
• Free/shareware Chromas software (Windows/DOS).