The Spatial Technologies Unit has been established in order to provide highly specific but also comprehensive services (from tissue or cells to data).

The extensive diversity of cutting-edge instruments enables researchers using the STU to use the optimal technology to a specific problem (and not the available technology), integrate different modalities, or even test across technologies. We at the STU will provide support from the project design to data interpretation in order to help you maximize findings and focus on the science.

Most projects start with a consultation. Feel free to email us or use the relevant form to initiate a project. All projects are on equal priority regardless of whether they are internal/external academic or industry.

Some major guidelines are presented below, while additional details will be provided, specific to the project and technology(ies) employed.

• Costs: In all preparations larger number of samples reduces costs. In Visium preps, the tissue optimization costs are spread across more samples, while in the assays requiring custom captures or antibody panels to be created, usually these reagents come in kits for 10 or 20 samples. The closer each experiment is to the kit size (8 or 16 for single cell, 4 or 8 for Visium, 10+ for Akoya, ~20 for MERSCOPE), the lower the cost per sample. We will work with you to find the optimal solution that can address your research question and fits your budget.

If you are interested in our services, please schedule a consultation via the contact section in this website. Prior to the consultation, please ensure that you and your team have the following information at hand:

• Main driving question for the project.
• Timeline.
• Tissue or tissues to be evaluated, species (e.g. human or mouse), and condition of the tissues (paraffin embeded (in blocks), FFPE (pre-cut slides), frozen, in OCT, or prospectively collected.
• Number of samples expected to be evaluated.
• Rough dimensions of the tissue section to be analyzed.
• Have you thought on the number of targets and which targets will be investigated ? (if the technology requires a probe set or antibody plex to be established)
• For single cell (not single nucleus), the number of cells, whether the viability of cells has been evaluated (e.g. is viability >90-95% after 1h on ice?)
• Will you require data analysis? Which aspects should it optimally cover?

During the consultation, the STU experts will provide guidance regarding the technology (or technologies) that can tackle the question at hand, given the sample quality and quantity available for the project.

We will also provide the STU’s Memorandum of Understanding (MOU), which provides a clear description of our role, capabilities, and pricing framework.

Clear quotes will be provided with respective timelines for each activity to maximize your ability to plan sample provision or other aspects of the study.

Finally, instructions for sample collection (if prospective) and shipping will be provided to ascertain best practice.

Sample Preparation

FFPE Tissue: Paraffin embedded samples are optimally kept in blocks at low humidity conditions. Please avoid pre-cutting the blocks, since it increases degradation. Use of desiccant bags along with the samples helps  during storage or shipment. In case the blocks need to be pre-cut, we recommend cutting the first few slides and providing for spatial analysis slides from deeper in the block to minimize the chance for degradation. Samples should be promptly shipped to the STU following cutting.

Frozen Tissue: Gentle freezing using an isopentane bath is preferable, while tissues embedded in OCT work usually optimally for most experiments. 10x Genomics provides a very detailed guide on sample preparation, which works for most technologies.

Shipping

The sample submission form must be filled at least two weeks prior to sample submission to allow for proper scheduling. Avoid shipping samples at the end of the week, we suggest that all shipments take place on Monday or Tuesday.

Frozen tissue samples or cells should be packed with adequate dry ice and be shipped with overnight shipping.

Paraffin blocks or freshly cut sections, should be accompanied with desiccant in boxes that minimize movement of the samples.

Please ship all samples (following notice) to:

Please mark clearly on the box the temperature of the samples (e.g. -80, -20, room temperature), and include in the box a sample sheet with clear indication of the sample ID(s), tissue/group, and main contact information.

For grants and publications, please follow the templates below for proper acknowledgment of service.

Level 1 – Assays and Analyses Performed:

“All X, Y, Z, experiments were performed at the Spatial Technologies Unit (STU), Beth Israel Deaconess Medical Center, Harvard Medical School Initiative for RNA Medicine (RRID:SCR_024905). Spatial tissue profiling and single cell data analyses were performed by support from the Spatial Technologies Unit personnel on the BIDMC Ithaca High Performance Computing cluster.”

Level 2 – Acknowledgment of services and specific personnel:

[Level 1] + “The Authors would like to thank [Insert Name Here] and the personnel of the Spatial Technologies Unit (STU), Beth Israel Deaconess Medical Center, Harvard Medical School Initiative for RNA Medicine (RRID:SCR_024905) for the ……”

For Contributions Beyond Fee for Service:

Payment of fees for services and authorship are not mutually exclusive and will be discussed prior to starting a project. We follow the general guidelines for authorship laid out by the International Committee of Medical Journal Editors. We’ll be happy to discuss with you whether a project goes beyond standard service provision.