Topic
Ambient RNA
Why does every cell express hemoglobin or the marker of a neighboring cell type?
Free-floating RNA from lysed cells is captured in every droplet and shows up as low-level expression of highly abundant transcripts across all clusters. Empty droplets tell you the ambient profile; SoupX, CellBender and DecontX estimate and subtract it.
- How to Detect Ambient RNA Contamination in Single-Cell RNA-seq
When hemoglobin, immunoglobulin or a neighboring cell type's markers show up in every cluster, the soup is talking; here is how to prove it before you annotate anything.