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Ambient RNA

Definition
AI-generated

Ambient RNA is extracellular or lysate RNA that is captured in a single-cell droplet or well together with a cell’s own transcriptome, contaminating profiles and inflating apparent expression of highly abundant transcripts outside their true cell of origin.

Topics
Single-cell analysis
Related
Doublet in Single-Cell Sequencing Pseudobulk Quality Control (QC)

Why it matters in GWAS

Poor ambient-RNA correction or high contamination can distort clustering, cell-type labels, and pseudobulk aggregates used for sc-eQTL mapping, weakening genotype–expression associations or creating spurious ones.

Example usage

"We ran an ambient-RNA removal step before building pseudobulk matrices for eQTL analysis."

Doublet in Single-Cell Sequencing Pseudobulk Quality Control (QC) RNA Sequencing (RNA-seq) Single-Cell Sequencing Unique Molecular Identifier (UMI)
Related-term network

Click any node to open that term page.

Node order. The current term is first. Next come every page linked from Related terms, in the same top-to-bottom order as that list. Then new terms appear in two-hop layers: for each of those direct neighbors (in that same order), their related terms are appended if not already listed. A third pass does the same for two-hop nodes. The walk stops when a fixed maximum number of nodes is reached.

References

  • Cuomo ASE, Nathan A, Raychaudhuri S, et al. (2023). Single-cell genomics meets human genetics. Nat Rev Genet. https://doi.org/10.1038/s41576-023-00599-5
  • Wolf FA, Angerer P, Theis FJ. (2018). SCANPY: large-scale single-cell gene expression data analysis. Genome Biol.
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