Internal Users: Submit your order request on the DNA Order Portal. Drop off samples in the KCBD (900 E. 57th) hallway freezer outside room 1230I (north end of east corridor) after submitting your request on the DNA Order Portal.

External Users:  Submit your order request on the DNA Order Portal. Ship your orders to Sanger DNA Core, University of Chicago, KCBD rm 1230H, 900 E 57th St, Chicago, IL, 60637. Share your order tracking details with us by either listing sanger@bsd.uchicago.edu as a contact for the shipment, including the shipping details in your order request, or forwarding your tracking information to sanger@bsd.uchicago.edu.

Billing questions may be directed to osrfbilling@bsd.uchicago.edu

DNA Template: Submit 4.5uL of template in a distinct well for each reaction. See the Template Preparation page for our recommendations on concentrations and preparation to achieve those concentrations.

High-Throughput Sequencing:

• Reactions must be submitted in strip-tubes or 96-well plates. External clients should seal plates with securely-fitting strip caps to prevent sample loss during shipping.
• Orders for core-supplied primers must contain at least 8 reactions per primer. Organize your submitted reactions by primer so that reactions with the same primer are adjacent to each other to facilitate multi-channel pipetting.
• Orders including custom primers must be submitted as template premixed with 3uL (4uM) primer for each reaction. A total of 7.5 uL of template + primer premix must be submitted per reaction. In the order spreadsheet use the term “premix” in the primer column. If you would like your primer included in the filename of your returned sequence, include the primer name in the Sample Name column.
• Ultra-hi sequencing rates apply to high throughput orders consisting of a minimum of 88 reactions.

Low-Throughput Sequencing:

• For orders including custom primers:
  • Submit custom primers (3uL at 4uM per reaction) in 1.5 mL tubes labeled with the primer name as entered in the order template.
  • OR submit reactions as template premixed with 3uL (4uM) primer for each reaction. Premix submissions to the core freezer should include 7.5 uL of premix in a distinct well for each ordered reaction. In the order spreadsheet use the term “premix” in the primer column. If you would like your primer name included in the filename of your returned sequence, include the primer name in the Sample Name column.

Tubes and plates:

DO NOT use flat-bottomed plates as they are difficult to pipette from. Samples should be securely sealed with strip caps. Sealing with most tapes (clear & metallic) WILL result in leakage unless the samples are dried down. For shipped samples it is especially important that the sealing method be secure against leakage, and samples packed to avoid crushing.

Reaction organization and labeling:

• Organize reactions to avoid gaps where possible.
• Please give samples and primers reasonably short names, avoiding more than a combined length of 23 characters.
• Label reactions in strip tubes, 1.5 mL tubes, and plates by the corresponding well position (A1, B1, C1…12F, 12G, 12H), NOT the sample name. Strip tubes and plates only require that the first reaction well of each be labeled.

Please also label each 1.5mL tube, strip tube, and plate with your PI’s first and last initial and your first and last initial.

We supply the following standard primers (at 4 uM):

• M13 (-21) Forward for 5′ GTAAAACGACGGCCAGT 3′
• M13 Reverse 5′ CACACAGGAAACAGCTATGACCAT 3′
• M13/pUC Forward 5′ CCCAGTCACGACGTTGTAAAACG 3′
• M13/pUC Reverse 5′ AGCGGATAACAATTTCACACAGGA 3′
• T7short 5′ TAATACGACTCACTATAGGG 3′
• T7term 5′ GCTAGTTATTGCTCAGCGG 3′
• T3 5′ AATTAACCCTCACTAAAGGGA 3′
• SP6 5′ ATTTAGGTGACACTATAG 3′
• SP6Long 5′ ATTTAGGTGACACTATAGAATAC 3′
• BGHrev 5′ TAGAAGGCACAGTCGAGG 3′
• CMV Forward 5′ CGCAAATGGGCGGTAGGCGTG 3′
• polyT-G 5′ TTTTTTTTTTTTTTTTTTTTTTTTTG 3′
• polyT-C 5′ TTTTTTTTTTTTTTTTTTTTTTTTTC 3′
• polyT-A 5′ TTTTTTTTTTTTTTTTTTTTTTTTTA 3′
• polyT(ACG) 5′ TTTTTTTTTTTTTTTTTTTTTTTTTA/C/G 3′

For large templates such as BAC’s, PAC’s and cosmids which can have higher levels of impurities, we recommend the use of the SP6long primer instead of the standard SP6 primer, which has a marginally low Tm. The SP6long primer is four bases longer (so check for compatibility with your vectors) but works well for large templates when the shorter SP6 primer fails.

Important Notes

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.

Files can be downloaded three ways:
1) Web browser (recommended)
2) FTP transfer in a web browser
3) FTP transfer by client program (eg: FileZilla).

When a new PI account is created, instructions for accessing the OSRF Cores server will be provided by email.

Web Browser

Web browsers (Safari, Chrome, Firefox, etc) can now be used to download individual files, several selected files, or entire folders (directories). Connect to the site and provide the username and the password that was provided to your lab at an earlier date (NOT your CNET ID). This should connect you within your lab directory. Click on folders to enter them, or on the download arrow to transfer them. Multiple single files can be selected using the checkbox on the right, then downloaded using the download button on the bottom of the screen. Note that multiple files will be transferred as a zip file archive.

FTP transfer in a web browser

A web browser can be used to transfer individual files using FTP by connecting to this address: https://coresdl.uchicago.edu. Provide your username and password that were given earlier (NOT your CNET ID) to connect. You will be able to transfer single files at a time.

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. 

Problems

If you encounter problems connecting, viewing or downloading your files, or if you wish to change your password, please email osrfhelp@osrfmailsrv.uchicago.edu.

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