Spatial Profiling Services Frequently Asked Questions
10X Genomics® Visium HD®
General Questions
1. What are the advantages of Visium HD compared to alternative spatial profiling options?
Visium HD is unique in offering researchers the ability to profile the whole transcriptome in high resolution across a 6.5 x 6.5 mm area of human or mouse FFPE tissue. There is no need to place regions of interest as the entire 6.5 x 6.5 mm area is captured.
2. Can GENEWIZ perform immunofluorescence (IF)?
We currently do not support the IF workflow for Visum HD. Each antibody requires optimization which is time-consuming and expensive for the customer. Instead, we recommend the customer perform Visium and IF on serial sections.
Panel Selection
3. Can probes be designed against my transgene/other custom transcripts?
We recommend using the off-the-shelf panel whenever possible, but it is feasible to spike-in probes against custom genes. 10x has prepared an SOP for designing the probes. There is no guarantee that custom probes will work, or that they will not negatively impact overall performance of the assay.
4. What sequencing depth do you recommend?
The recommended sequencing depths are as follows: FFPE – 275 M reads/sample; fresh frozen – 700 M reads/sample; fixed frozen tissues – 500 M reads/sample. However, this sequencing depth should be seen as a starting point, and deeper sequencing is recommended to detect less abundant transcripts.
Sample Preparation
5. What sample types are compatible with Visium HD?
Currently, FFPE, fresh frozen, and fixed frozen materials are compatible with Visium HD. We accept pre-cut sections mounted to slides. Alternatively, you may submit FFPE blocks which we will section on your behalf.
6. What are the sample requirements?
If you are submitting pre-cut sections, we request 2-3 slides, each containing a 5 µm thick section, as well as a 1.5 ml tube containing FFPE scrolls for sample QC purpose. Refer to your quotation and our sample handling guide for complete details. If submitting an FFPE block, we will perform sectioning on your behalf. Please ship FFPE blocks and slides at room temperature or on wet ice.
7. What QC is performed prior to Visium HD?
TapeStation will be run on RNA extracted from a parallel section or an adjacent region of the tissue. It is recommended to only process samples with DV200 > 30%.
8. Can archival samples be processed?
Yes! We recommend submitting sections immediately after sectioning, but archival (previously H&E-stained) sections and pre-cut sections as old as 6 months are compatible if stored correctly.
9. Can you return my FFPE slides/blocks after Visium HD processing?
Tissue sections occasionally become damaged or destroyed during the Visium HD workflow. However, upon request, GENEWIZ will return all slides after processing. If providing FFPE blocks, please note that they may be exhausted after sectioning, but we will take every effort to preserve material and return blocks after processing.
Contact
10. How do I contact GENEWIZ for a technical consultation about my project?
GENEWIZ's NGS Team is composed of Ph.D. scientists who can help you optimize your project design and provide consultation. Contact the team directly by emailing us at NGS@genewiz.com, or calling us toll-free at 877-GENEWIZ (436-3949) ext. 1.
Data Analysis & Delivery
11. Can you perform CLIA- or GLP-grade analysis on the:
Visium HD Platform?
The Visium HD workflow is available under our Regulatory Environment (Reg-E) service level with a Research Use Only (RUO) report. This entails utilizing qualified equipment, trained personnel, and full documentation and chain of custody throughout the process.
GeoMx Platform?
Digital spatial profiling using the GeoMx platform is currently provided on a research use only (RUO) basis. Please contact our CLIA Team by emailing us at CLIA@genewiz.com, or calling us toll-free at 877-GENEWIZ (436-3949) ext. 1 if you're interested in clinical-grade digital spatial profiling.
12. What data delivery methods are available?
GENEWIZ will recommend the best data delivery option based on your specific project details. Data delivery options include:
- Secure File Transfer Protocol (SFTP)
- Customer cloud account
- External hard drive (additional charges may apply)
13. How will my data be delivered?
If your results are being shipped to you via hard drive, you can track its shipment using the tracking number provided to you in the delivery email sent from GENEWIZ.
If your results are being delivered via another data delivery method, such as AWS S3, Aspera, or other cloud-based methods, please refer to the delivery email sent from GENEWIZ for detailed information on the transfer, and consult with your IT department to ensure compliance with your institution’s policies.
If your results are being sent via a secure File Transfer Protocol (sFTP), please refer to GENEWIZ’s sFTP Data Download Guide for instructions on how to download your data and troubleshooting tips.
Ordering & Processing
14. How do I request a quote?
For a quick tutorial, watch the video below. Select the Spatial Genomics icon to reach the quote request form.
15. What happens after I submit a quote request form?
Our NGS team will review your inquiry, follow up with a quote, and guide you through the next steps.
16. How do I confirm a quote?
For a quick tutorial, watch the video below.
17. How do I submit the GENEWIZ Sample Submission Form to provide detailed information about my samples?
Please watch the video below for a brief tutorial on how to submit your Sample Submission Form.
18. How can I monitor the progress of my project?
The status of your order, including an estimated date of delivery, can be viewed anytime through your GENEWIZ account. Visit the Order Summary page of your project to find the current order status. Watch the video below for a brief tutorial.
19. How long does GENEWIZ hold samples?
We hold samples for 1 year after project completion. Please contact us if you would like samples retained for a longer period or shipped back to you.
Have a specific question?
Contact Us | Phone 1-877-GENEWIZ (436-3949), ext. 1