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How to submit samples
This document is a step by step guide explaining how to submit samples. It includes the following topics:
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How to access the Sample Submission Form from Nanuq
How to fill in the Sample Submission Form
How to submit the Sample Submission Form in Nanuq
How to track a submission in Nanuq
What tube and plate types are acceptable
Sample preparation specifications
Sample and primer organization
How to send samples to the Sequencing Service
It is important to follow the instructions described in this document in order to avoid processing delays.
Step 1 - Accessing the Sample Submission Form from Nanuq
1. Enter the following address: https://genomequebec.mcgill.ca/nanuqAdministration.
2. Enter user name and password which was issued upon account opening.
3. Click on ‘Sequencing’ to access the Sequencing Platform Menu.
4. Select ‘Submit Samples’ for sequencing within 2 to 4 working days or ‘Submit Samples in BaseXpress mode’ for
sequencing within 24 hours.
5. Select the type of service required; sequencing or DNA preparation for the extraction and sequencing of plasmid DNA
from bacterial colonies.
6. Indicate whether or not the SNP (Single Nucleotide Polymorphism) discovery service is required. This service includes
sequencing, data analysis and the production of a report. Additional information about this service is provided on the
website.
7. Indicate the type of container that the submitted samples will be in. A 96-well plate is required for all submissions
totalling 48 samples or more.
8. Click on ‘Download Excel Template’.
9. Open the Sample Submission Form in Microsoft Excel or OpenOffice.
Step 2 - Completing the Sample Submission Form
The information provided in the Sample Submission Form is necessary for the proper and efficient sequencing of
samples.
It is important to read the header in the Sample Submission Form in order to:
● verify that the correct form is being used,
● access instructions to complete the form,
● be aware of the required sample concentrations and volumes,
● access the list of primers provided by the Sequencing Service,
● be aware of the permissible tube and plate models.
1. ‘Purchase Order Number’ field
A purchase order number obtained from your institution’s accounting department must be entered if the payment option
chosen was purchase order number. Note that this option was chosen when the account was opened.
2. ‘Plate or Tube Set Name’ field
A name must be given to each plate or tube set. This name must be unique and cannot exceed 50 characters. In
addition to alphanumeric characters, the hyphen ( - ), underscore ( _ ) and period ( . ) are permissible however accents
and blank spaces will not be accepted.
3. ‘Sample name’ and ‘Primer’ field
Names cannot exceed 50 characters. In addition to alphanumeric characters, the hyphen ( - ), underscore ( _ ) and
period ( . ) are permissible however accents and blank spaces will not be accepted.
Sample Names
Sample names must be entered in the column entitled ‘Sample name’ in the following order: A01 to A12, then B01 to
B12, etc. and not A01, B01, C01, etc with empty rows between the sample names.
The names must be unique.
If you would like the primer name to appear in the chromatogram file name (i.e., the file ending with the extension ab1)
then it must be included in the sample name.
Primer
Primer names must be entered in two places
Primer names must be entered in the ‘Primer’ column. Only one primer is permitted per cell. If a sample is to be
sequenced with more than one primer then that sample name must be entered in the ‘Sample name’ column as many
times as it needs to be sequenced. Then all associated primers must be listed in the ‘Primer’ column.
The purpose of this is to indicate which primer must be used to sequence the sample listed in the ‘Sample name’
column. See example in the screen shot below.
Primer names must also be entered in the ‘Sample name’ column. For this primer name list ONLY the ‘project name’
and ‘Type of DNA’ columns must be filled-in.
The purpose of this is to provide the technicians with the physical location of the primers.
Primer : Enter
only one primer
per cell.
Sample name :
Enter a unique name for each sample.
Enter the required primer name for this
sample in the column entitled ‘Primer’.
4. Chose the appropriate DNA type from the drop-down list in the ‘Type of DNA’ column.
Type of DNA :
If the type of DNA is
primer, only the Sample
Name and Project Name
columns are required.
5. Enter the PCR product or plasmid size in the ‘Size of template (base pairs)’ column.
6. The project name is case sensitive therefore it must be entered exactly as it appears on the Homepage.
7. Additional information pertinent to sequencing may be entered in the ‘Information on DNA’ column.
Download sample files
[Excel] Sample Submission Form – sample and primer organization in a 96-well plate
[Excel] Sample Submission Form - sample and primer organization in PCR “strip” tubes
Complete and save the file in an easily accessible folder.
Step 3 – Submitting the Sample Submission Form in Nanuq
All samples to be sequenced must be submitted electronically through Nanuq.
Return to the page entitled ‘Sequencing Samples Submission’ and follow the instructions described in ‘Step 3- Upload
Excel File’ on Nanuq’s webpage.
Check mark the box ‘BaseXpress’ for all samples to be sequenced within 24 hours.
For more information about the BaseXpress service, most notably the latest acceptable drop-off time and price, it is
important to read the document entitled ‘What is the BaseXpress service?’.
Nanuq will then validate the submission as described below in step 4.
1. Sample validation FAILED! Nanuq will list all the errors found. Once the errors have been corrected, save the file
and click on ‘Upload the same file again’.
Errors listed as 1 and 2:
These errors were generated because the ‘Type of DNA’ chosen in row 23 was primer. Nanuq understands this to mean
that the entry in ‘sample name’ (i.e., PCR2_P1) is the primer name and does not expect to find an entry in ‘Primer’
column nor ‘Size of template (base pairs)’ column.
To correct this error change the entry in ‘Type of DNA’ from primer to either Not purified PCR or Purified PCR, whichever
is appropriate.
Error listed as 3:
This error was generated because the project name in row 33 does not appear exactly as it was written on the
Sequencing Services Request Form. If the project name originally included capital letters they must appear in this entry.
To verify the project name return to your Homepage on Nanuq.
To correct this error change the entry in ‘Project name’ from endymion to Endymion.
Error listed as 4:
This error was generated because there is an entry in ‘Project name’ and ‘Type of DNA’ columns however there is no
entry in ‘Sample name’ of row 37. Nanuq expects to find a primer name listed in the ‘Sample name’ column.
To correct this error list the name of the primer in the ‘Sample name’ column.
Do not hesitate to contact us if any problems should arise.
2. Validation successfully completed! Verify that the summary information is accurate, specifically the total number of
samples and information entered into the Excel sheet. To complete the submission click on ‘Confirm Sample
Submission’. If this is not done the submission is not logged in Nanuq. In order to make a correction, return to the
‘Sequencing Samples Submission’ page by clicking on ‘Cancel’.
The sample submission confirmation page, which follows, includes the submission number generated by Nanuq. This
submission number is very important as it may be used to follow the progress of your samples and will be needed as a
reference for all submission inquires.
All questions with respect to a submission are directed to the contact person listed on this page. It is therefore important
to confirm the accuracy of this information.
From this page it is possible to :
• Print the waybill. It is mandatory to include this waybill with the samples.
• Submit new samples
• View the submission lot
The bar code is
scanned once the
samples have
arrived to the
sequencing lab.
BaseXpress must appear on
the waybill in order for the
samples to be processed
within 24 hours.
Step 4 – Tracking a submission in Nanuq
The ‘Sample Submission Search’ page is available from the sequencing platform menu. This page lists all submissions
and associated information, namely, number of samples, their status, plate name, etc.)
Additional submissions may be made from this page.
To view submission details on the ‘Samples Submission Lot’ page click on the sample submission lot number.
From this page it is possible to :
• Print the waybill.
• Remove the submission by clicking on ‘Delete Lot’. This function remains available until the sequencing group
accepts the samples.
• View the submission status by clicking on the view samples icon.
o Samples will remain logged as waiting for approval till they get to the sequencing laboratory.
o Samples are logged as accepted the day of their reception.
o Samples will be logged as rejected if the submission requirements are not followed or if they arrive in poor condition
o Samples will be ignored upon your request.
o Samples results are available on Nanuq for those logged as sequenced.
Step 5 - Acceptable tube and plate formats
Only certain plate and tube models are compatible with the Sequencing Service procedures.
These accepted plate and tube models are:
• PCR “strip” tubes
• PCR 96-well plates
• PCR 384-well plates
Suggested products :
• PCR “strip" tubes: UltiDent Scientific, 0,2 ml thin-walled 12 tube and domed cap strips, catalogue number: AB-1113
• PCR 96-well plates: Axygen Scientific, 96-well half-skirt PCR microplate clear, catalogue number: CA47743-952
• PCR 384-well plates: Corning, Thermowell Gold PCR Plates, catalogue number: 3757
• Plate sealers: Applied Biosystems, MicroAmp Clear Adhesive Films, catalogue number: 4306311
A 96-well plate must be used for all submissions of 48 samples or more.
Step 6 – Preparing Samples
Volume and concentration required per sequencing sample:
Volume
Unpurified PCR
20 μl minimum
Purified PCR
7.5 μl minimum
Concentration
PCR amplifications must be verified on an agarose gel and
a copy of the gel picture must be sent to the sequencing service
with the samples.
PCR products of less than 250 bp result in lower quality
sequences due to an oversaturation phenomenon whereby they
appear much more intense than usual and to the compression of
bases at the beginning of the sequencing read, which is an inherent
limitation of the 3730xl technology.
PCR products greater than 2000 bp can be difficult to
sequence because the concentration of DNA submitted is
generally too low. The longer the PCR products the higher DNA
concentrations are required to achieve good quality
sequencing.
Volume
Plasmid DNA
or phage
BAC/PAC end
sequencing
Concentration
7.5 μl minimum
100–500 ng/μl
20 μl minimum
500 ng/μl minimum
Step 7 – Organizing Samples
Samples must be organized in the plate/tubes in precisely the same way as they were in the Sample Submission Form.
The tubes must be identified using their well position from the Sample Submission Form: A01, A02, A03…and not their
sample names nor primer names.
Samples and primers must be aliquoted in separate wells as many times as they will be used even if a sample or a
primer is to be used multiple number of times.
The primers must be aliquoted precisely in the same order that the samples, they are to be used with, are in.
Step 8 – Sending Samples
The samples with their WayBill must be sent by mail or delivered in person between 9:00 AM and 5:00 PM, Monday to
Friday.
BaseXpress service samples must arrive to the Sequencing Service before 11:00 AM, Monday to Friday.
Samples must be addressed to:
Sequencing Service
McGill University and Génome Québec Innovation Centre
740, Dr-Penfield Avenue, Room 7300
Montréal, QC, H3A 0G1
Tel: 514-398-3311, ext. 00522
Fax: 514-398-1795
Do not hesitate to contact us if any problems with the sample submission should arise:
By email: [email protected]
By telephone: 514-398-3311 ext. 00522