Illumina Library Submission

In Order to Get Into the CAT Illumina Sequencing Queue

  1. Your sample tube should be labeled with the iLab Service ID generated after you submit online.
  2. Submit a sequencing request and access the submission form through iLabs.
  3. If you don't have an iLabs account already, you can review the account creation guide and create an account.

  4. Request services, select the appropriate sequencing run configuration (see the service descriptions), and complete the sequencing submission form.

  5. See the Data FAQ for additional instructions for preparing your submission and what to expect in return.

    Need to make changes? If you need to alter your service or request details after submission, do not cancel or create a new request. Instead, email [email protected] with your Service ID in the subject line. This helps us maintain your place in the queue and keeps our records clean.
  6. There is some required information.
    1. The average size of the library (in base pairs), as seen on the Bioanalyzer/TapeStation/Fragment Analyzer traces.
    2. Default PhiX spike in is 0.5%. If you need more than this for low-diversity libraries, list the %. Note that smaller libraries preferentially cluster compared with the 450bp-sized PhiX library, so you may need to request a higher PhiX% to reach your target.
    3. In the sample/barcode table, Names can only include letters, numbers, dashes, and underscores. Barcodes must be uppercase and can only contain A, C, T, G, and N (for UMI sequences).
    4. If you need custom primers, special index read output, demultiplexing options, or if there is something weird to note about your library, select the appropriate checkboxes.

Submitting samples/tubes to the CAT Core

  1. Sample Tube: For a single lane of Illumina sequencing, put 30ul of your sample in a 1.5ml low-bind tube at 5-10nM (this is around 1.5-3ng/ul). If your library is below 5nM, please increase the volume to 40 ul. If your sample is greater than 20 nM please dilute it. For each additional sequencing lane, please add 20 ul of the library. Label the cap with your ServiceID and the side with the date. 
  2. Custom primers: add 20 ul of a 100 uM aliquot of the custom primer to a 1.5ml tube. Label the primer tube with the last three digits of your service ID + sequencing read. For example, "123 R1" for a Read 1 primer or "456 I2" for an Index Read 2 primer.
  3. Drop off sample:

Drop off the Sample Tube and any Custom Primers (if needed) in the small freezer in the mail room on the second floor of Genentech Hall. The room is 221, and it is by the main staircase.

  1. Shipping samples:

Place 1.5ml tubes in a secondary container like a 50ml conical with kimwipes to prevent samples from jostling. Ship via UPS or FedEx to:

Eric Chow

S252 CAT Lab

600 16th Street

San Francisco, CA 94158

 

Referencing the CAT Core and Publications

 

When submitting manuscripts, please acknowledge the CAT by including the text: “Sequencing was performed at the UCSF CAT, supported by UCSF PBBR, RRP IMIA, and NIH 1S10OD028511-01 grants.” 

 

To aid our facility in future grant submissions, it helps to reference labs and publications that have benefited from our core please notify us of your achievement by emailing catcore [at] ucsf.edu the PMID number, lab, and the piece of equipment used in the paper.