Bulk RNA-seq
- Cheaper
- Simpler
- Statistically stronger with replicates
Suitable for: ✔️ Homogeneous samples (like cell lines) ✔️ High-throughput designs with many conditions ✔️ Studies where replication is key (e.g., drug treatments, time-course) ✔️ Situations where per-cell resolution won’t change your biological conclusion
Single-Cell RNA-seq
Use scRNA-seq if your question depends on:
- Detecting rare populations
- Disentangling heterogeneous tissues
- Discovering cell-type-specific signals
In these cases, resolution matters—and scRNA-seq earns its price tag.
But know this: you’re trading off simplicity, QC, and replicability.