TITLE: Plate Preparation and Submission (Eurofins)
AUTHORS: Dakota Betz

[DESCRIPTION]
This protocol details how to set up a plate for sequence submission, from the initial spreadsheet preparation and sample naming scheme, to physical plate preparation and submission to the eurofins website/shipping.

[STEPS]
SECTION: Spreadsheet Preparation
1. Log in (lab credentials) to eurofins.genomics.com. Navigate to Plate Sequencing and select Order Now for Standard Plates. Download the Excel spreadsheet by clicking on the icon.
 

SECTION: Spreadsheet Preparation
2. If applicable: type the Plate Barcode (found on the sticker you will afix to the plate) into the spreadsheet at the top (no hyphen). Also replace the tab name (currently set to "Plate 01") with the barcode. Select PCR Products for "Sample Type" and Standard for "Advanced Options". Leave all other settings default.
 
SECTION: Spreadsheet Preparation
3. Set primer to Premix for all samples.
SECTION: Spreadsheet Preparation
4. Add sample names in the following format (NO SPACES):
 

 

SECTION: Spreadsheet Preparation
4.1. Your "four letter code" is unique to you and can be any of the following, but please PICK ONE and do not change it once you've used it for a plate. It should be the same for every sample/plate belonging to you:
first 4 letters of your first name
first 4 letters of your last name
first 4 letters of your UCSD email
 

SECTION: Plate Preparation
6. If you have not done so already, dilute your primers for use on the plate (1:10): use 1 µL and 9 µL for each sample that you have (if you scaled this protocol, amounts should be adjusted for your number of samples to accommondate 1uL of Primer and 9uL of water for each sample). Note that your personal primer stock is already diluted from the original primer stock, but you must dilute again for this step.
 

 

SECTION: Plate Preparation
7. Check that you have the appropriate primers (diluted) and samples thawed and mixed prior to starting. Arrange primers and samples (PCR products) so that they match the order of your spreadsheet before starting.
SECTION: Plate Preparation
8. Pipette 10 uL Diluted Primer into the appropriate wells (check your spreadsheet). Add 5uL of the appropriate PCR Product into each well (one PCR product per well). 
 

SECTION: Spreadsheet Preparation
5. Print out the plate spreadsheet and bring a copy with you before proceeding to Plate Preparation.
SECTION: Plate Preparation
9. Make notes as necessary on your printed spreadsheet as you go. If you make a mistake, note it right away. You may have to adjust the remaining spreadsheet layout in order to accommodate an error--if so, add notes to ,ry clear what you did. You can then edit the plate spreadsheet after you've finished prepping the plate.
 

SECTION: Plate Preparation
10. Affix strip caps to filled columns in the plate, label the right side of the plate if necessary (see note about plate barcodes in step 2), and put the plate in a plastic bag. Seal and store in the refrigerator (or in the -20°C freezer for long-term storage if not shipping for 2 or more days) until ready to ship.
 

SECTION: Plate Submission
11. Revisit your plate spreadsheet with your notes in hand. Make edits to the excel document as needed to accommodate any mistakes or changes that you made during plate preparation.
SECTION: Plate Submission
12. Once the plate spreadsheet is complete, upload it to the Eurofins website (use the Browse tool available on the same page as the spreadsheet download -- see step 1). The upload will be checked for errors before you can proceed to the next page.
SECTION: Plate Submission
13. Eurofins will create a schematic diagram of your plate with associated sample names (hover over the green circles). Spot-check this schematic with your spreadsheet to make sure it is correct.
SECTION: Plate Submission
14. Click Submit/add to cart. Keep all options as the defaults. Make sure you've selected the lab credit card as the payment option. Make sure that Print Digital Shipping Label is selected whenever it appears.
SECTION: Plate Submission
15. Upon checkout, you should be prompted to print the shipping label. Attach the shipping label to the outside of one of the padded envelopes, and place the confirmation (which printed with it) inside the envelope with the plate. Drop off at any UPS location (don't forget to ask for a receipt).