Schumer lab: Submitting libraries for sequencing

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Submitting libraries for sequencing

We do most of our sequencing at Admera health [1]. We also sometimes submit libraries to PAN[2] on campus for MiSeq sequencing.

Submitting libraries to Admera

  • send 10 ul to the sequencing facility and keep the rest in the -20C freezer here
  • fill out the admera health form with
    • Delivery: Your name/Schumer Lab, 371 Jane Stanford Way, Schumer Lab Room 318, Stanford, CA 94305
    • Bill to: Pamela Hung, 371 Jane Stanford Way, Stanford, CA 94305
    • leave PO info blank (Pam has an account set up)
    • Service: Copy description from quote you recieved
    • kits: none (we have already done the library prep)
    • Admera Health Quote no.: put in quote number
    • data transfer method: ftp link (this is the fasted method, you can download data to oak using wget or cyberduck)
    • special instructions: any info you want them to have, for example: these are three pools each to be ran on a separate lane
    • library and pool ID columns should be the same for each pool (one row filled out per pool)
    • library type as appropriate and sample type is usually tissue
    • insert size including adapters: "total library size: x bp" using tapestation peak size
    • Phix %: 1% is a standard spike-in amount. the purpose of Phix is to serve as a control to make sure the sequencing reaction worked. It can also help balance indixes. However, the more Phix you spike in, the less data you will get
    • index sequences: one row for each library in a pool, Admera can use either the sequences or the reverse complements as long as you adjust the column heading to say which you are providing.
  • if this is your first time shipping somehting using dry ice take the dry ice training on axess (EHS-PROG-2700)
  • send Pam the filled out sheet and request a fedex overnight shipping label for a package with about 3kg of dry ice that is about 5 lbs and addressed to:
Admera Health, LLC
126 Corporate Boulevard
South Plainfield, NJ 07080
Attn: Biopharma Services
  • Make sure your 1.5ml tubes of library or library pools are secured either in a 50ml conical tube with kimwipes or a taped sample box and place them in a styrofoam cooler (there should be some stashed above the glassware cabinet) with dry ice (on the second floor of gilbert)
  • ship the cooler and a printed out copy of the sample submission sheet in a cardboard box with all old shipping labels/barcodes removed.
  • print out three copies of the fedex label pam sends to you.
  • attach one label to box using the fedex shipping pockets in the mail room and place a dry ice sticker (also in mail room) on the box
  • leave box on fedex table and 2 extra copies of shipping label in the folder on the table.
  • fedex pick up is at 2:30

Submitting libraries to PAN