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Article

The effect of background noise and its removal on the analysis of single-cell expression data.

Genome biology - 19 Jun 2023

Janssen Philipp, Kliesmete Zane, Vieth Beate, Adiconis Xian, Simmons Sean, Marshall Jamie, McCabe Cristin, Heyn Holger, Levin Joshua Z, Enard Wolfgang, Hellmann Ines

Abstract excerpt

BACKGROUND: In droplet-based single-cell and single-nucleus RNA-seq experiments, not all reads associated with one cell barcode originate from the encapsulated cell. Such background noise is attributed to spillage from cell-free ambient RNA or barcode swapping events. RESULTS: Here, we characterize this background noise exemplified by three scRNA-seq and two snRNA-seq replicates of mouse kidneys. For each...

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Identifiers

PMID: 37337297
DOI: 10.1186/s13059-023-02978-x
PMCID: PMC10278251

Provenance

PubMed metadata and Literature Corpus relationships. Corpus snapshot updated 7 Sept 2026. Manifest publication-graph-cohort-2026-09-07.1.

Source receipt: pubmed, retrieved 7 Sept 2026.

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