A practical guide to designing publication-ready expression profiling pipelines.
Single-cell RNA sequencing has opened a window into cellular heterogeneity that bulk RNA-seq simply averages away. But single-cell is not a universal upgrade — it answers a different question, at a different cost.
What bulk does well
Bulk RNA-seq remains the workhorse for differential expression between conditions when the tissue is reasonably homogeneous. It is cheaper, deeper per gene, and statistically simpler.
When to go single-cell
If the biology lives in rare cell populations, developmental trajectories or shifting cell-type proportions, single-cell is the only way to see it. The trade-off is shallower per-cell depth and more demanding analysis.
- Bulk — condition-level differential expression
- Single-cell — cell-type resolution and rare populations
- Spatial — expression in tissue context
Choose the resolution your hypothesis needs — then design depth and replication around it.
Our team builds reproducible pipelines for both, from QC and normalisation to publication-ready clustering and trajectory figures.