Writing a Successful Single Cell RNA Sequencing Grant Proposal

Many scientists rely on grants to perform cutting-edge research.

Innovative scientific ventures push the boundaries of biological and medical sciences by harnessing state-of-the-art technologies, methodologies, and data analysis.

Single cell RNA sequencing (scRNA-Seq) is a powerful method to investigate gene expression at the individual cell level. It has provided new answers to decades-long quests in biological and medical sciences.  When adopting scRNA-Seq, researchers can discover rare cell populations, characterize cell types, and decipher cellular differentiation and reprogramming mechanisms.

For these reasons, scRNA-Seq-based research increasingly prevails over bulk RNA sequencing as the method of choice (Fig.1).

Government agencies know the value scRNA-Seq technology brings to the scientific community. Indeed, each year, they award millions of dollars in multidisciplinary grants to scRNA-Seq studies and the infrastructure surrounding them.

But writing a scRNA-Seq-centered grant has its own set of challenges. It is a technical field, and not all grant reviewers may know it in depth. Moreover, scRNA-Seq experimental planning requires an optimized sample preparation and analysis strategy.

To support scRNA-Seq grant writing, consider these tips when authoring a grant proposal.

Single cell RNA-Seq is the method of choice for identifying the heterogeneity and complexity of RNA transcripts within individual cells in tissues or organs.

Stem cells and dormant or circulating tumor cells are often present in low quantities but unique from the predominant cell types in a sample. These low abundance types are lost if running traditional, bulk RNA-Seq.

In cell development and disease progression, gene expression changes and evolves over time. Identifying individual cell stages, such as stem cells versus differentiated cells or immune cells in different activation states, reveals developmental trajectories and regulatory networks with exceptional granularity.

Developing cell atlases in all living organisms has enormous potential as they can reveal cell types’ identities, functions, and regulations. Atlases help characterize cellular and molecular reactions to various stimuli, including drugs, pathogens, or environmental factors. Additionally, they offer insights into the distinctions between cell types across species or individuals.

Single cell RNA-Seq technologies are the best tool for research questions interrogating biological phenomena with finer granularity.

When the applicant identifies measurable objectives and selects scRNA-Seq as the best technology, there are some additional guidelines to include when preparing for a successful scRNA-Seq grant proposal:

• Describe the scRNA-Seq Technology
• Demonstrate an Understanding of Sample Preparation
• Show Preliminary Data
• Define the Data Analysis Plan

The most successful applications will contain all these elements. Addressing each directly exhibits completeness of consideration to the effort required, scoring well with reviewers.

Describe the scRNA-Seq Technology

Grant reviewers come from different backgrounds covering the various aspects of a grant application—not all of them may be versed in scRNA-Seq technology. The methods section is an opportunity to provide a complete description of the technology principles.

There are two main types of scRNA-Seq methods: instrument-based and instrument-free.

Instrument-based methods were the most common, as they were the first to be commercially available. But the ability to scale up experiments is limited to the instrument’s capacity. Therefore, increasing the experimental size requires instrument upgrades or multiple replicates of the same sample, drastically increasing the budget and experimental complexity.

The leading instrument-free approach relies on combinatorial barcoding. This approach is feasible in any biology lab. Complex or large experimental designs become independent of core lab schedules by incorporating fixation, a built-in feature of combinatorial barcoding. Parse Biosciences’ Evercode(™) technology has commercialized this approach, making it easy to get started in scRNA-seq for any biological lab.

Regardless of the technology chosen, reviewers want to understand how the technology operates and what the final output will look like.

It’s a good practice to ask the company providing the technology to write a letter of support, committing to technical assistance throughout the project.

Demonstrate an Understanding of Sample Preparation

A successful scRNA-Seq experiment relies strongly on good sample preparation. Poor results often stem from issues with creating a single cell or nuclei suspension.

Tissue samples require dissociation to obtain a single cell suspension before starting a scRNA-Seq experiment. An appropriate dissociation protocol minimizes cell aggregation, loss, and death, thereby maximizing cell viability.

To ensure successful dissociation, careful planning, and testing are necessary for all samples, including tissues, cell lines, and organoids. However, certain tissues, like skin biopsies, are particularly challenging to digest and demand additional care and specialized protocols.

Many examples of suspension protocols are available from research communities, publications, and single cell companies.

Show Preliminary Data

Pilot studies are small-scale studies to inform experimental feasibility and workflow. Reviewers strongly weigh preliminary data in an application. The best pilot studies address the risk of the experimental approach. When supported by a promising example study, time, cost, and effect size are easier to justify.

The study design emerging from the pilot will impact the number of cells sequenced, samples analyzed, and sequencing depths. These factors ultimately impact timing and budget. It is a good idea to involve a computational biologist at this early stage. They will help optimize the experimental design, including the minimum necessary sample size for an informative study.

Core facilities are a tremendous resource for providing grant information and support. Some cores offer grants to kickstart grad students or young investigators’ proof-of-concept development.

Define the Data Analysis Plan

A clear and detailed data analysis plan confirms the experimental design can answer the research question. If the approach is well validated, references pointing to previous works suffice.

Including a detailed description of the bioinformatic tools and analysis software is a best practice. Discuss expected outcomes, potential challenges, limitations of the proposed pipeline, and alternative approaches that may be necessary for unpredictable results.

Single cell RNA sequencing knowledge aside, polished grant proposals require time to author. According to the NIH, preparing for a grant takes at least two months.

Multiple people —with different writing styles and voices—often collaborate to complete the proposal. Creating a refined grant proposal with a unified voice will require numerous rounds of revisions.

For this reason, create a grant writing timetable and track progress to keep preparation and writing on track. Several project management tools, such as Monday.com, Asana, and ClickUp, offer free accounts and academic discounts to manage the collaboration required of top-performing grants.

To ensure all pieces of the grant preparation and submission come together, the first investigator usually doubles as the project manager. Managing accountability across a team is a practiced skill that requires regular follow-ups, understanding, and problem-solving. Hosting a daily or weekly check-in with collaborators is recommended to manage progress and setbacks.

The writing style is as important as the project itself. Ultimately, the writer must convince the reviewers of the proposal’s value. A persuasive style – like the Toulmin model – presents a clear and logical argument for why the project deserves funding. This style is instrumental in the abstract, as it is the first thing the reviewers read and influences their predisposition toward the rest of the proposal.

Before clicking the send button, a final check to ensure all links work and attachments are present is always a good idea.

And don’t forget to celebrate the submission! Regardless of the funding decision, submitting a grant proposal is a significant accomplishment in its own right. Take your team out for a treat or find some other way to reward the effort.

Scientific research is the best job in the world, and grants are part of it. They can be challenging, definitely frustrating, and very competitive.  But there are many helpful resources; hopefully, this article is one of them.