FAQ

How can we initiate a collaboration?

As with all Broad Platforms, we act as scientific partners, engaging deeply in the project from conception to analysis to publication. We will be happy to share our expertise with your team, including inherent challenges, pitfalls, and optimization guidelines that are not always obvious, which can make the difference between a good idea and a successful experiment. Continued engagement will also ensure that your project has access to cutting-edge tools and methodologies we develop far in advance of publication.

Regardless of the stage of your project, email us (stpconsultation@broadinstitute.org) a brief description of your project to schedule an introductory meeting with one of our senior scientists. To guide the discussion, it is helpful to arrive at the meeting with the following information:

What is the overall goal of the project? What question do you hope spatial can answer?
What is the model system?
Approximately how many samples do you have available? How physically large are they? If they have already been collected, how were they preserved?
What other data have you collected from these samples (especially RNA-seq/scRNA-seq)
Share any images you have of your samples H&E, immunofluorescence, ISH. If you don’t have any of your samples, a literature example can still be very helpful.
A comment on your comfort level with bioinformatics, images, and custom analysis.

At the end of the meeting, the platform scientist will recommend next steps at the STP, if possible, or will steer you to one of the other possible avenues:

Recommend a small scale pilot project to evaluate feasibility, providing a quote, and outlining the division of work between you and the platform.
For systems where the platform has experience, recommend jumping into a full scale project and advise on reagent generation.
Direct you to an area core facility; or an academic collaborator (below)
For unfunded projects or novel capabilities, forging an academic collaboration, usually in the form of a grant application

The scientist and one or more research associates will stay with you throughout for consultation as needed. We encourage you to reach out with questions as they arise, whether strategic or technical. It is nearly always easier to advise or troubleshoot through regular communication rather than after the project is already long underway.

What happens next?

Once an overall scope has been agreed on and a quote has been funded, our team will work with you to section samples as appropriate for the indicated study. This can be done either by us or by a pathology facility of your choosing with our guidance. We will also ask you to set up a google bucket or Terra.bio workspace for your project so we can deliver the data back to you. Samples or slides are then transferred to us using a courier or hand delivery and enter our queue for staining and imaging with the discussed platform. Once we generate data, we will deposit it to the destination provided with the identifiers you provide. Data typically includes raw files, QC metrics from the instrument, and in the case of the RNA methods, preliminary cell by gene matrices.

Throughout the process, you will get direct email updates from the research associates running the samples, who are typically the technical experts in each method. If we decide to run the data in batches, we will be available for interim meetings where we will present QC metrics and share impressions before proceeding to the next batch.

We will return blocks and unstained slides back to you at the end of the project, and will delete data from our servers once you have confirmed receipt.

While we do not offer analysis services, after data delivery, we are available for consultations and will share workflows we have developed for common analysis steps. These questions may be handled by the platform scientists and research associate, or, occasionally, by computational scientists familiar with the data type.

Note: while we work with human samples frequently, we require that they be completely de-identified before. We assume that our users have ensured spatial profiling is approved by their IRB.

What are your prices?

Please refer to our latest pricing here, or email stpconsultation@broadinstitute.org to inquire for more information.

If there are limited-time promotional discounts available through one of the companies, we will lower prices to reflect that.

Do you make your microscopes available for self service?

We permit self-service by internal Broad users on our mesoSPIM light-sheet, our Andor Dragonfly spinning disk confocal, and our Nikon TI2 epifluorescent microscope. If you’re a Broad internal user you’ll need to get trained on these. External users can reach out to use the microscopes as an academic collaboration, depending on our bandwidth. We do not give walk up access to our spatial hardware, as they are too precious to our pipeline.

When does it make more sense to work with an academic collaborator?

Many of the methods offered at the STP were developed by labs in the local area, who are by definition the experts in their field. The STP offers these methods to provide extra bandwidth beyond what the originating labs can offer, but any potential user is welcome to seek out a collaboration with the inventors. If bandwidth at the home lab is an issue but the inventor would like to still be involved, we are open to three way arrangements where the inventor provides interpretation and guidance but the work is performed at STP.

When does it make more sense to run the method yourself?

Generally speaking, building the methods out in your lab only make sense if you are comfortable with a large scale investment and plan to make spatial data generation the major component of what your lab does. We estimate that a typical new method in the field requires >$1,000,000 to start up, and requires continued, heavy investment in personnel with diverse skill sets to keep running. Large scale projects can be set up more quickly at the STP, while small scale projects can be accessed more easily and cheaply from the STP and Flow Facility.