> ## Documentation Index
> Fetch the complete documentation index at: https://docs.synthesize.bio/llms.txt
> Use this file to discover all available pages before exploring further.

# Usage Examples

> Example prompts and practical guidance for writing better gene expression analysis requests in Claude.

# Usage Examples

The best prompts clearly state the two groups you want to compare and, when relevant, the sequencing modality.

## Prompt patterns that work well

Use prompts like these:

```text theme={null}
Use Synthesize Bio to compare gene expression between heart and liver cells.
```

```text theme={null}
Use the Synthesize Bio connector to analyze lung adenocarcinoma tumor vs normal lung tissue.
```

```text theme={null}
Analyze CD4+ T cells vs CD8+ T cells in single-cell RNA-seq mode using Synthesize Bio.
```

## How to make prompts better

Include the details that matter most:

* the two groups to compare
* whether the request is bulk or single-cell
* the tissue, cell type, disease context, or condition

## Tips

* Keep the comparison focused on two groups.
* Use direct comparison language such as `A vs B`.
* If you want biological interpretation after the analysis, ask for it in a follow-up prompt.

## Example follow-up prompts

After the analysis is complete, users can continue with questions like:

```text theme={null}
Summarize the top up-regulated and down-regulated genes in plain English.
```

```text theme={null}
Explain which pathways seem most relevant based on these differentially expressed genes.
```

```text theme={null}
Turn the result into a short research-style summary I can share with my team.
```

If a user runs into issues, continue to [Troubleshooting](./troubleshooting).