Schumer lab: Submitting libraries for sequencing

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

• make sure that your library or pooled library is within the size range you want using the tapestation and is around 4nM using the Qubit and the nM conversion spreadsheet in box (https://stanford.app.box.com/file/418914060874)

• 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