Submit Samples

Use the form below to submit your samples for Spatial Transcriptomics.

This will inform our services team of the expected arrival of your samples and provide us with the necessary information for processing. Upon submission, you will receive a confirmation email automatically.

If you have any inquiries regarding the sample submission, please do not hesitate to contact us or refer to our sample requirements page.

Your details - Step 1 of 12

Please ensure you have the following information prepared before starting your sample submission:

1. Contact Details

Your contact details
Customer code
Not signed up as a customer yet? Please click here to sign up.
Don't remember your customer code? Please send an email.

2. Financial Information

Quotation number
PO number
PO document

3. Project Information

Information can be found on the quotation.
Always refer to your quotation while completing the sample submission form.

4. Sample Information

Biosafety/GMO status
Sample details

5. Data Handling

Data contact details (name and email)
Species to map to
Additional mapping requirements
⚠️ Warning: If sequences are not provided during sample submission but are provided afterwards, an extra mapping fee will be charged.

Info before starting sample submission *

I have all the information ready

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Customer Details

Name Project Contact *

First

Last

Email Project Contact *

Confirm Email

Phone *

Customer Code *

You received a customer code from us via email when you signed up on our website. The subject of the email is "Welcome to Single Cell Discoveries".

Not signed up as a customer yet? Please click here to sign up.
Don't remember your customer code? Please send an email.

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Financial Information

Quotation Number *

Enter the number on the quotation, the document with a statement of the costs of service that you received from us.

Don't have a quotation yet? Please request a quotation before submitting your samples. The quotation needs to be signed electronically for us to be able to proceed with the sample preparation.

Budget Number *

PO Number *

A purchase order (PO) should be provided by your financial department. If you don't have a PO yet, please contact your financial department with the quotation you have received from us. Without a PO we cannot process your samples. For more information please click here.

Upload PO Document *

Click or drag a file to this area to upload.

Upload the PO document (pdf only).
Please allow for the file to upload completely before clicking next. This may take a minute. The progress bar will disappear once complete.

Additional finance information

If you have additional information you need us to put on the invoice (such as a specific budget number), you can use this field.

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Biosafety Information

Any presence of GMOs in the submitted samples? *

Genetically modified organisms (GMOs) are organisms in which the genetic material has been altered in a way that does not occur naturally. This includes any complex changes of the DNA, such as transgenes or other genetic additions.

Please specify which samples contain GMOs *

Please provide information about the host organism, vector used and the genetic insert of the GMOs *

BSL-1 safe? *

Yes
Yes, pathogen was inactivated
No

Can samples be safely handled within a standard BSL-1 laboratory? Biosafety level 1 (BSL-1) applies to laboratory settings in which personnel work with low-risk microbes that pose little to no threat of infection in healthy adults.

Upload Biosafety Documentation *

Click or drag a file to this area to upload.

Warning: When you are providing samples in which a pathogen was inactivated, please provide documentation to show how this was achieved. Include experimental data demonstrating that the pathogen is not harmful anymore.

Please allow for the file to upload completely before clicking next. This may take a minute. The progress bar will disapear once complete.

⚠️ Warning: Unfortunately we can currently only process samples that can be safely processed at BSL-1 level. Please contact our lab team at lab@scdiscoveries.com, to discuss the options.

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Shipping Information

Number of Slides or Tissue Blocks *

How will the samples be shipped? *

Shipment via courier
In-person delivery at our visiting address in Utrecht, the Netherlands
SCD delivery service

Only select SCD delivery service if you are located within the Utrecht Science Park and this service is included on your quotation.

⚠️ Once your samples have shipped, please contact our lab team at lab@scdiscoveries.com to forward the shipment tracking number or inform us of any shipping delays.

Which courier will you use? *

If other, please specify which courier. *

What is the expected shipping date? *

We recommend shipping packages on Mondays or Tuesdays.

Please review our shipping information page before sending your samples.

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Service Details

Service *

Sample type *

Preservation Method *

If other, please specify preservation method. *

Spatial Transcriptomics Service *

Please refer to your quotation.

Add-on(s) *

Tissue sectioning
DV200 QC
Morphology Assessment (DAPI/HE staining)
None (please provide DV200 value in sample sheet)
Other

Select all that apply. Only select the options indicated on your quotation.

If other, please specify the add-on. *

Sequencing Depth *

Please refer to your quotation.

Please specify the total sequencing depth. *

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Sample Quality

To ensure the tissue to be used is of high enough quality, a DV200 QC check should be performed on mock tissue slices originating from the the same tissue block the actual samples come from. Tissues used for Visium HD Spatial Gene Expression work should have a DV200 of >30%. In case samples have a DV200 of less than 30%, an additional check by morphology assessment with DAPI and H&E staining can be performed to assess the risk of using the sample.

Before our lab team starts processing samples with the 10x Genomics protocol, a careful quality check (QC) of the cell suspension(s) is performed. Please be aware that samples that do not meet QC requirements will NOT be processed.

Fixed RNA profiling (Flex) samples fail QC when:

Viability is lower than 50% prior to fixation

Not enough cells/nuclei are present

If your samples don't reach the minimum DV200 requirement, please send an email to our lab team for more information.

Confirmation quality *

I understand and I agree

Do you want samples with a DV200 score of <30% to be run with the Visium HD pipeline? ? *

No, only run on samples when DV200 score of mock samples is >30% (recommended)
Yes, and I accept the risk of failure
Yes, but only specific samples, and I accept the risk of failure

Additional remarks regarding the quality

It is important that the supported type of glass slides is used for mounting the samples to be analysed with the Visium HD pipeline. Failure to use the right slide type will compromise the sample, leading to tissue detachment during the workflow. Supported glass type brands and product numbers can be found on the sample requirements page.

Please select which glass slide type was used for the provided samples *

If other, please specify the glass slide used (product name, product number, brand) *

Regarding the information about glass slide use *

I understand and I used Visium HD supported glass slides
I understand, I have used different glass slides but I understand the risk of sample loss.

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Data Details

Please let us know to whom we should send the sequencing data. This is also the person who will receive the instructions on downloading the raw sequencing files for further analysis.

Name Data Contact *

First

Last

Email Data Contact *

Confirm Email

Species *

If other, please specify which species. *

Will the dataset contain data from multiple species? *

Second species to map *

If other, please specify which second species *

Additional remarks regarding data analysis

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Download the sample sheet

Download the sample sheet by clicking on the Excel icon below. Complete the fields and upload the form on the next page. Please do not forget to SAVE the form and PRINT it to include it in the sample shipment.

This sheet is essential for our lab team to correctly identify the samples.

Click here to download the sample sheet

If you cannot complete the sample sheet now, please use the save and resume later button below to save your submission.

You will receive an email with a link to later resume with your sample submission.

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Upload the sample sheet

Upload your sample sheet *

Click or drag files to this area to upload. You can upload up to 4 files.

Please allow for the file to upload completely before clicking next. This may take a minute. The progress bar will disappear once complete.

Additional remarks regarding the sample submission sheet

If known/available: Upload your Regions of Interest (ROI)

Click or drag files to this area to upload. You can upload up to 4 files.

For information on ROI, please read ROI selection. Please allow for the file to upload completely before clicking next. This may take a minute. The progress bar will disappear once complete.

Additional remarks regarding the ROI(s)

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Confirmation

Visium HD sample requirements *

I confirm that my samples adhere to the Visium HD sample requirements.

10x Genomics vial type *

I confirm that the glass slide type that is used is in accordance with the sample requirements.

Vials clearly labeled *

I confirm that the sample containers / slides are clearly labeled with appropriate labels and/or markers.

Shipping instructions *

I confirm the samples will be shipped with cold packs and according to the shipping instructions.

Storage for 6 months *

I understand that samples will be disposed after 6 months of storage at Single Cell Discoveries, if not processed before that time. Counted from the date of arrival.

Print confirmation *

I confirm that I will include a printed version of the Excel sample sheet with the package.

Comments

If you have any specific comments on this submission, please let us know.

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Your form entry has been saved, and a unique link has been created which you can access to resume your sample submission.

Enter your email address to receive the link via email. Alternatively, you can copy and save the link below.

Please note this link will expire in 30 days. Afterwards, your form entry will be deleted.

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Email *

FAQ

Which samples are compatible with Visium HD?

Currently, we accept Formalin-Fixed and Parafin-Embedded (FFPE) samples only. Visium HD Spatial Transcriptomics is compatible with human and mouse samples. We accept tissue slides and tissue blocks.

What glass slides should I use for mounting the tissue sections?

It is crucial to use supported glass slides only, as using unsupported glass slides will result in tissue detachment and sample loss during the Visium HD workflow. You can find supported glass slides in our sample requirements page.

How many mock slides should I provide for QC testing?

To be able to assess RNA quality, we will ask you to provide additional 5-10um sections in a microtube. For large tissues (>6.5mm x 6.5 mm) 1 or 2 sections are enough. For smaller tissues (<6.5mm x 6.5 mm) please provide 4 sections.

How should I prepare my tissue sections for analysis?

We recommend carefully reading the 10x Genomics Visium HD tissue preparation Handbook (page 43 and onwards). If there are any questions or doubts about the preparation, do not hesitate to get in touch with your SCD representative.

How should I send you the samples?

Check the shipping guidelines for shipping Visium HD samples on our sample requirements page.

What can we help you with?

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Submit Samples

Customer Details

Financial Information

Biosafety Information

Shipping Information

Service Details

Sample Quality

Data Details

Download the sample sheet

Upload the sample sheet

Confirmation

FAQ

Let's discuss
your research

Fast, high-quality
Sequencing Service

Transcriptomics
within tissue context

Data Consulting
as a service

State-of-the-art
RNA solutions