Submitting Samples Online

Primers

SimpleSeq & Sequencing Dashboard

Results

How to download results

I. Submitting Sequencing Tubes Online

General guidelines for submitting in tubes

These guidelines apply to samples submitted in tubes from SimpleSeq Kits or other custom sources.

1. Suspend templates in water only as other buffers may inhibit the sequencing reaction (in particular, excess amounts of EDTA)
2. When you prepare 'Premixed' samples, ensure that your template has been purified prior to mixing with primers
3. We strongly recommend the use of barcode labels on all tubes. Tubes from the SimpleSeq Kits are pre-labeled with barcodes. You can also get free barcodes from Eurofins Genomics. This will be shipped using USPS at no cost to you. Order these barcodes ahead. If you decide to label the tubes using a sharpie or marker, ensure that the letters are legible and clear.
4. When using custom centrifuge tubes to send your samples, ensure that the tube-size is equal to or greater than the 1.5-mL centrifuge tubes, unless you are using SimpleSeq Tubes. It is sometimes difficult to decipher the label on smaller tubes, which can result in extending the processing time.

Click on each of the tube sequencing service to find guidelines related to the specific sequencing service.

SimpleSeq^TM Kits, Premixed

The SimpleSeq Premixed kit can be used only for submitting premixed damples. One sequencing reaction will run under Standard Read conditions using the sample from each tube. To place an order using the SimpleSeq^TM Kit, Premixed service, you must do the following:

• Stock Solutions: Prepare aqueous stock solutions of purified Templates and Primers as described in Table 1
• Assemble 'Premixed' Samples: Assemble the premixed samples as described in Table 2, Sample Preparation Guidelines; simply pipette the required volumes into the barcode-labeled split-sealed tubes
• Ship Samples: Ship the samples to Eurofins Genomics, DNA Sequencing Lab
• Download Sequence Data: Our QA team will send a message when your samples have been porcessed. You can then login to download the sequence data.

Please note that you do not need to provide any order information online. One sequencing reaction will be performed on each sample. Additional services, such as DNA preparation or PCR Purification cannot be requested for orders involving SimpleSeq Premixed sequencing services.

SimpleSeq^TM Kits, Standard and Custom Tube Sequencing

The SimpleSeq^TM Standard Kit provides the most economic and efficient solution for a wide range of sequencing services provided by Eurofins Genomics. You can avail a variety of sequencing services when you submit samples in the barcoded-tubes from the SimpleSeq Standard Kits or your 1.5-mL/2-mL centrifuge tubes. The table below highlights the various sample types, sequencing services offered for samples submitted in tubes (either from SimpleSeq Standard kits or Custom tubes).

Accepted Sample Types based on		Types of Sequencing Chemistry Offered	Number of Sequencing reactions per sample tube	Additional Services Offered
Sequencing Service	Nature of the template
'Premixed'Samples 'Templates Only' Samples 'Templates and Primers' Samples	Plasmids BACs Purified PCR Products Crude PCR Products Clones	Standard read Power Read	Single Multiple	DNA Preparation PCR Purification Custom Primer Synthesis Sent Primer Storage

Please note that only 96, single Standard Read services can be redeemed when using tubes from a single SimpleSeq Standard kit. Additional services, such as PCR Purification, or upgrades, such as Power Reads, incur addition costs that will need to be paid during checkout.
To order sequencing services for sample submitted in barcoded tubes from SimpleSeq Standard Kits:

1. Stock Solutions: Prepare stock solutions as described in Table 1
2. Label Tubes: Label your sample submission tubes
   • SimpleSeq Tubes are pre-labeled with Barcodes.
   • Paste the barcoded labels procured previously from Eurofins Genomcis (These barcoded labels are shipped to you free of cost when ordered through Eurofins Genomics).
   • Use a marker to label in clearly legible letters. Please note that additional handling charges may apply.
3. Assemble samples: assemble your sample in the labeled tubes based on the type of sequencing services required (refer to Sample Preparation Guidelines, Tables 2, 3, 4 or 5 for the relevant information)
4. Manual Entry: Provide the details of your sample and required services using the Tube Sequencing order editor. The guidelines here are provided for the manual entry process only.
• Sample Type: choose the sample type based on the nature of the template. Your samples can be Plasmids, PCR Products or Large Contructs (BACs/Fosmids/Cosmids). Please note that the sample type is defined at order level. To submit a mixture of samples, add one sample type to the card and then add the second sample type, before checking them out together.
• Add. Service: PCR purification is available for PCR products and DNA Preparation is available for Plasmids and Large Constructs.
• Pre-Mixed with Primer: click on the box to indicate if your samples are premixed, all the sequencing primer fields will then be disabled.
• Template Size/Product Length: the Template Size/Product length is used in the lab for two independent purposes: a)Power Read services, and b)Quality Control (particularly when the size of the template is smaller than the typical read length).
• Send a Primer: When you send 'Templates and Primers' samples, ensure that that the primers are sent separately in tubes. Please follow the guidelines to assemble the sent primer. Enter the name of the sent primer (and barcode, when applicable) and add the primer to the list. You can the choose the primer in the dropdown list. Please refrain from using SimpleSeq tubes to send your primers.
• Order a Primer: There are over 75 universal primers that are available for your use at no charge, however, when you submit 'templates only' samples and require the synthesis of a custom primer, you can use the 'order a primer' control. Simply name the primer, enter the sequence and hit 'Add Primer to List/Cart'. The primer name will then appear on the dropdown list and be added to the cart. For multiple custom primers, repeat the process. The synthesized primer(s) will then be used in the sequencing reaction and stored in our laboratories for your future use (upto 250 sequencing reactions or 6 months)
• Provide Sample Level Details: You can enter the rest of the details about your sample and the sequencing reaction conditions required in this section of the order editor.

  Barcode	Template Name	Sequencing Primer	Options
  Remember to include the barcode on the SimpleSeq tube or on the free label pasted on the tube. Without this number, your SimpleSeq sequencing services will not be redeemed. Hit the 'Fill all' button to populate the fields sequenctially with the available barcode numbers.	Provide a unique name for each template sample. Ensure that the barcode is appropriate for that sample. When you hit the 'Fill all' button, a number is appended to the name of the sample and incremented to fill the template name fields.	Select a sequencing primer from the dropdown list. When your order a primer or send a primer, these are automatically added to this dropdown. To manage the the standard and shared primers that appear on the the dropdown list, go to the my Favorite Primers tool.	You can add other features to the sequencing reaction/sample. Add multiple reactions for sample submitted in one tube Choose Power Read sequencing chemistry. The default choice is standard chemistry Add sample specific notes(optional) delete the sample

5. Upload Template (substitute step 4): You can also place the order using the Excel upload form. Download the form, provide information in the required fields based on the 'Helpful Tips' page and upload the form at the order editor. The data provided by will be captured by the tube sequencing order editor. Provide any additional information and proceed to checkout. Go to the tube sequencing order editor and upload the filled template.
6. Checkout and Shipping: You will not be charged for any standard redeemed services (SimpleSeq Kits), all other services will be priced. When you proceed to checkout, you will be prompted with Eurofins Genomics Dropboxes, within 30 miles of your labs location. Where available, you can drop your samples in the drop box before the specified time. Otherwisem, you can use any UPS/other carrier location to ship the samples to Eurofins Genomics, DNA Sequencing Lab.
7. Download Sequence Data: once the QA team has verified the processed sequence data, these sequencing results will be available from your login account. Please note that you can share these results with the members of your group using the Group Admin Tool.

General Guidelines for submitting in plates

Assembling the Samples: These guidelines apply to samples submitted for any of the plate sequencing services, including Ready2Load, ShortSeq, and custom/prepaid plate sequencing services.

1. Samples should be assembled and shipped in 96-well, v-bottom, Full-skirt PCR plates
2. Please attach a barcode label to each plate for unique identification. The Prepaid Plates are prelabeled.
3. It is strongly recommended that two wells (Wells H11/H12 for the 'By Row' layout or G12/H12 for the 'By Columns' layout) in each sample-carrying plate are left empty. These will be used to load internal quality control samples.
4. Only strip caps provide the most secure shipping conditions (we do not recommend foil or tape-seals; this can result in cross contamination or sample loss).
5. Enter the details of the sample online.
6. Ship the strip cap-sealed 96-well plates to the DNA Sequencing lab or drop the same in the Eurofins Genomics Dropbox (when located near you).

Editing/Uploading the Excel templates to Place Sequencing Orders: When filling and uploading the Excel templates for different order editor, please adhere to the following suggests to reduce the number of potential upload errors:

1. Correct Excel Template: Ensure that the correct template is being uploaded at each order editor. The excel templates from the legacy Operon site cannot be used here.
2. Valid Characters: It is easy to accidentally insert invalid characters into the primer name or DNA name fields. Accepted characters include letters (A-Z, a-z), numbers (0-9), and an underscore or dash.
3. Empty Wells: To leave wells empty, simple leave the corresponding fields empty. Do not deletw the well.
4. Plate Name: The name of the sheet in the excel template is the name of your 96-well plate. Change the names of the sheet on the template accordingly. Use alphanumeric characters in the name of the sheet.
5. Refrain from editing pre-populated texts in the templates: The text in the cells with blue background in each sheet of the Excel templates are configured to be recognized by the e-commerce site. Refrain from making any changes in these pre-populated cells.
6. Select from dropdown lists: We recommend that you choose the options from the dropdown lists rather than type in the text manually. The lists provided in the excel templates have been synched with the lists in the e-commerce order editor (except for stored/sent primers).
7. Additional Plates: Each sheet in the excel template is considered to be a 96-well plate. To add additional sheets, make a copy of a sheet. You can upload information about samples in 20 different plates with each upload.

Click on each of the Plate sequencing service to find guidelines related to the specific sequencing service.

Ready2Load Plate Sequencing Service

Prepare your Ready2Load samples based on the guidelines provided in the Preparation of 'Ready2Load' samples section of the Sample Preparation guidelines. The predefined features of the Ready2Load plate sequencing service include:

1. Applies only to samples assembled Post-BigDye reaction.
2. Only the sequencing gel will be run for the provided samples
3. Per Plate pricing.

To place an order for Ready2Load plate sequencing service, the following steps must be followed:

1. Prepare DNA templates prepare the templates based on the recommendation set forth in the manual accompanying the BigDyeterminator v3.1 Cycle Sequencing Kit.
2. Perform Cycle Sequencing use the BigDye Terminator v3.1 Cycle Sequencing Kit and a thermocycler to run the sequencing reaction. The BigDye terminator kits are currently being sold by ThermoFisher scientific. Use the product documentation to ensure that the cycle sequencing reaction is performed based on the recommended guidelines.
3. Purify Reactions: ensure that the unincorporated nucleotides are removed from the reaction mix.
4. Load Samples: load the purified sequencing reaction mixture into the wells of a 96-well plate.
5. Provide Sample Related Information: Download the Ready2Load Plate sequencing template and enter the relevant information. Read the General Guidelines (Plate Sequencing Services) before making changes in the Excel Template.
   
   • Label the plate use a sharpie or marker to label the plate. Name the excel sheet based on this label
   • Sort Plate: Select the arrangement of samples based on the how you have assembled the 96-well plate.
   • Provide the sample level details in the following format

     Well Position	Sample Name
     This column is filled based on the choice you make on the Sort Plate field. Do not try to edit these cells.	Provide a unique name for each sample loaded in the wells of the 96-well plate

6. Checkout:Proceed to checkout. The Ready2Load sequencing service is charged 'per plate'. When possible try to submit upto 95 samples in one plate.
7. Ship Samples: If you have a Eurofins Genomics dropbox near you, place the properly sealed samples there; otherwise, ship the sample to the DNA Sequencing Lab.
8. Download Data: Once you receive the email from confirmation that your samples have been processed, you can download your sequence data by logging into your account.

ShortSeq Plate Sequencing Service

ShortSeq Plate sequencing service, formerly, Express Plates is a service suitable for Premixed samples requiring short read lenghts (typically <550 bp). The predefined features of ShortSeq plate sequencing service include:

1. Standard Read chemistry
2. Read Length ≥550 bp
3. Applicable only for Premixed samples
4. Minimum 24 Premixed samples
5. Single reaction/sample in well
6. Rapid turnaround times (typically, before noon the day after the receipt of the samples)
7. Per plate pricing. To avail a sample-level price, use custom Plate Sequencing service or the tube sequencing services.

To place a ShortSeq Plate sequencing order, the following steps need to be followed:

1. Prepare Stock Solutions: prepare stock solutions as described in Table 1.
2. Assemble 'Premixed' Samples: Assemble the premixed samples as described in Table 2 (sample Preparation Guidelines) in the 96-well plates arranged in rows or columns.
3. Provide Sample Related Details: Provide the details of the samples and the sequencing reactions in the ShortSeq Plate Sequencing template. Follow the general guidelines (Plate Sequencing services) when entering/selecting data in the excel templates.
   • Plate level details: Provide the details of the samples submitted in the plate. These details provide a general descritpion of the samples.
     

     Entry	Description
     Sample Type:	Indicate the type of sample by selecting one from the dropdown list.
     Sort Plate:	choose the plate layout based on how you have assembled the samples. Choose 'By Rows' to enter data in the following order, A1, A2, A3, A4.

   • Sample level details: Since these samples are premixed and read using the standard chemistry, the only information required the process the samples in the well position and the sample name.
     

     Well Position	Sample Name
     This column is filled based on the choice you make on the Sort Plate field. Do not try to edit these cells.	Provide a unique name for each sample loaded in the wells of the 96-well plate

4. Upload Excel Template: upload the filled template at the ShortSeq Plate Sequencing order editor. You can verify the details of your sample after the information has been extracted from your template into the e-commerce site. Verify the data and proceed to checkout.
5. Checkout: Proceed to checkout. If you have a have a Eurofins Genomics dropbox located near your address, this will show up during checkout.
6. Ship/Drop the samples Place the samples in the dropbox or ship the same to the DNA Sequencing Lab (Residents of US - Eurofins Genomics, DNA Sequencing services, 12701 Plantside Drive, Louisville, KY 40299; Residents of Canda - Eurofins Genomics, DNA Sequencing Serivices, 700 Bay Street, Suite #1100, Toronto, ON M5G 1Z6.

Prepaid Plate Kits and Custom Plate Sequencing services

The Prepaid Plate kit sequencing service and custom Plate sequencing services provide a high level of customization in terms of the sequencing services and additional services offered. The table below highlights the various sample types, sequencing services offered for samples submitted in 96-well plates.

Accepted Sample Types based on		Types of Sequencing Chemistry Offered	Number of Sequencing reactions per sample in a well	Additional Services Offered
Sequencing Service	Nature of the template
'Premixed'Samples 'Templates Only' Samples 'Templates and Primers' Samples	Plasmids Purified PCR Products Crude PCR Products	Standard read Power Read	Single Multiple	DNA Preparation PCR Purification Custom Primer Synthesis Sent Primer Storage

Please note that different Prepaid Plate kits have different redeemable services. Additional services will incur additional costs.
To order sequencing services for samples submitted in plates:

1. Stock Solutions: Prepare stock solutions as described in Table 1
2. Label Plates: Label your 96-well plates
   • Prepaid Plates are pre-labeled with Barcodes.
   • Paste the barcoded labels procured previously from Eurofins Genomcis at the bottom side of the plate (These barcoded labels are shipped to you free of cost when ordered through Eurofins Genomics).
   • Use a marker to label the plate in clearly legible letters.
3. Assemble Samples: Prepare your sample in the 96-well plate based on the type of sequencing services required (refer to Sample Preparation Guidelines, Tables 2, 3, 4 or 5 for the relevant information)
4. Provide Sample Related Details: Provide the details of your sample and required services in the Plate Sequencing excel upload template. Read the general guidelines (Plate Sequencing Service) before editing the excel templates.
• Plate Level Details: Provide the details of the samples in each plate in each excel sheet. These entries describe the general properties of the samples submitted for the plate sequencing order.

  Entry	Description
  Plate Barcode:	If you are using a Prepaid Plate kit, enter the barcode attached to the side of the plate here to redeem those services during checkout. For custom 96-well plates, you can paste the free barcoded-labels from Eurofins Genomics at the bottom of the plate; enter that barcode here. If you do not have a barcode label, leve this field empty.
  Sample Type:	Choose the sample type based on the nature of the template being submitted in the plate. Accepted templates include Plasmids, PCR Products or a Mix of Both. Please note that you can submit different samples types requiring different additional services using different sheets of the excel file.
  Construct Size/Product Length:	Select the approximate range of the size of the samples.a If the range of the sample falls out the predefined reanges, you may indicate that on the plate notes.
  Add. Service:	PCR purification is available for PCR products and DNA Preparation is available for Plasmids.b
  Advanced Options:	By default, the Standard Read chemistry is used to sequence your samples. We offer Power Read services for difficult to read segments of the template.
  Template Specification:	Choose this only when you request for Power Read options. Select the feature which you have identified is the primary reason why the sequencing of the template can be challenging.
  Plate Layout:	Simply by choosing the two options in the dropdown, you can populate the well positions based on the way you decide to load your samples. Choose "By Rows" if you want to fill your samples sequentially from A1 to A12, before moving on to B1.

  ^aConstruct Size/Product length is used in the lab for two independent purposes: 1) Power Read services, and 2) Quality Control (particularly when the size of the template is smaller than the typical read length).
  ^bAdditional charges may apply
• Sample Level Details: You can provide the sample level details in each of the rows in the excel template. Please follow the recommendations below to provide this information.
  

  Well Position	Sample Name	Primer 1	Sequence to synthesize or Barcode for enclosed primers	Additional Columns
  A1, A2 ... or A1, B1 ... will be filled based on your plate layout choice	Enter a unique sample name for each sample-containing well in the 96-well plate.	Critical: you must provide a primer name. You can either: select the desired universal primer/'Premixed' from the dropdown Type in the name of the custom Primer to be synthesized Type in the name of the enclosed primer Type in the name of the Stored primer (please note that the name of the stored primer is case sensitive and should be typed in correctly to avoid any confusion).	The entries in these fields depend on the Primer column: For 'premixed', stored or standard primers, Leave this empty. For ordering a custom primer synthesis, enter the sequence of the primer. For sent/enclosed primer, enter the barcode number (if applicaple) or leave empty. Caution: If you enter a sequence, the same will be ordered.	information for upto 4 sequencing reactions for sample in each well. Follow the guidelines as described in the left.

  You can also place the order using the Excel upload form. Download the form, provide information in the required fields based on the 'Helpful Tips' page and upload the form at the order editor. The data provided by will be captured by the plate sequencing order editor. Provide any additional information in the following steps and then proceed to checkout.
5. Upload Excel template: follow the general guidelines when entering the data in the excel template and upload the same at the order editor. Please note that you can enter data in multiple sheets.
6. Verify Information: Once the excel template is uploaded on the order editor, you can provide any information that is not already provided. On step 3, you can verify the details of the sample and edit the samples in the third step, if required. You can proceed to the checkout. You will not be charged for any standard redeemed services (Prepaid Plate Kits), all other services will be priced.
7. Checkout and Shipping: When you proceed to checkout, you will be prompted with Eurofins Genomics Dropboxes, within 30 miles of your labs location. Where available, you can drop your samples in the drop box before the specified time. Otherwisem, you can use the UPS location to ship the samples to Eurofins Genomics, DNA Sequencing Lab.
8. Download Sequence Data: once the QA team has verified the processed data, these sequencing results will be available from your login account. Please note that you can share these results with the members of your group using the Group Admin Tool. Please note that when you order multiple sequencing results for the sample in each well, the sequence data will be delivered with a 1, 2, .., n appended to the name of the sample.

II. Primers

General guidelines for primers

Sample and Primer Storage

Samples are stored at our facilities for 5 days after they are processed. Please verify your sequencing results anc speak to our support staff at the earliest. When you need us to store your template samples for a longer period, please let us know by adding a comment to the order or notes for the plates or tube samples.

Besides the collection of standard primers, please note that we can store primers sent or ordered by you for your use. These primers will be available for use in your subsequent orders as long as there is sufficient quantity of the primer and the order is placed before the expiry date. Please ensure that you enter the name of the stored primer accurately. Errors in the names of the stored primers can lead confusion and delay of orders.

Primer Type	Default Storage (Days)	Extended Storage (Days)	Ordering sequencing services with stored primers
Sent primer (formerly, enclosed)	5	30 (when selected)	Choose the primer from the dropdown list or type in the name accurately in the excel template. Please note that the list(s) on the excel template(s) is not synched to your list on the online order editors. You will not be charged for the use of a stored primer. On expiry of the storage days or the quantity of the primer, the status of the primer will be 'archived', and will not be available for subsequent use.
Ordered primer	180	N/A
Free Standard Primers	Indefinite	Indefinite	Simply choose these from the dropdown on the excel template or the online order editors.

III. SimpleSeq & Sequencing Dashboard

General information on for the sequencing dashboard

The Dashboard is Your Home for Sequencing

The sequencing dashboard is one of the most exciting new features. It provides a centralized hub to handle all your sequencing needs. You can check how many reactions are available on the account, share kits with others, and navigate to other important areas such as sequencing results and order pages.

• Manage
• Manage reactions, FlexReads, SimpleSeq kits, Prepaid Plate kits, Free Barcodes and more.
• View
• The dashboard puts you in control with a full 360 degree view of everything going on with your kits and barcodes. You can view who is using each tube, which primers were used, status changes and more.
• Share
• Share kits with other people by using the sharing and assigning controls in the sidebar.

IV. Results

How to download results

Sequencing Results are Downloaded from the Order History Page

Whenever your sequencing results are complete, the results are uploaded as a zip file automatically and stored on a secure server. The zip file is downloaded from the order history page. Navigate to the order history page, expand the order, and click the link inside.