Illumina Library Submission

In Order to Get Into the CAT Illumina Sequencing Queue

  1. Your sample tube should be labeled with your iLab Service ID that is generated after you make an online submission.
  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 description of services), and complete the sequencing submission form.
  5. There are 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 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 the same length for all samples. If you are mixing single index libraries with dual index libraries, you'll need to fill out the constant sequence for the second index position. This is usually AGATCTCGGT.
    4. If you need custom primers, special index read output, demultiplexing options, or there is something weird to note about your library, select the proper check boxes.

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 lower than 5nM, please increase the volume to 40ul. If your sample is greater than 20 nM please dilute it. For each additional sequencing lane, please add an additional 20ul of the library. Label the cap with your ServiceID and the side with the date. 
  2. Custom primers: put 20ul of a 100uM aliquot of the custom primer in 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:

Bring the Sample Tube to the CAT and any Custom Primers (if needed), in the small freezer on the ground outside the CAT Core's double doors. This is near room S271 of Genentech Hall.

  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:

UCSF CAT Lab Attn: GH-S252

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.