Article

Ambient RNA analysis reveals misinterpreted and masked cell types in brain single-nuclei datasets

2022-03-11

Abstract excerpt

Ambient RNA contamination in single-cell RNA sequencing (RNA-seq) is a significant problem, but its consequences are poorly understood. Here, we show that ambient RNAs in brain single-nuclei RNA-seq can have a nuclear or extra-nuclear origin with distinct gene set signatures. Both ambient RNA signatures are predominantly neuronal and we find that some previously annotated neuronal cell types are distinguished by a...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: ceb6987c-c2a6-55ee-9121-f27bf7f7611d
DOI: 10.1101/2022.03.09.483658

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

Ambient RNA analysis reveals misinterpreted and masked cell types in brain single-nuclei datasetsDOI 10.1101/2022.03.09.483658Read

Transcriptomic diversity of cell types across the adult human brainSemantic proximity Read

A single-nuclei RNA sequencing study of Mendelian and sporadic AD in the human brainSemantic proximity Read

Single nucleus sequencing fails to detect microglial activation in human tissueSemantic proximity Read

A global view of aging and Alzheimer’s pathogenesis-associated cell population dynamics and molecular signatures in the human and mouse brainsSemantic proximity Read

Benchmarking ambient RNA removal across droplet and well-plate platforms reveals artificial count generation as a critical failure mode of scAR and CellClearSemantic proximity Read

ABACUS: A flexible UMI counter that leverages intronic reads for single-nucleus RNAseq analysisSemantic proximity Read

Avoiding false discoveries: Revisiting an Alzheimer’s disease snRNA-Seq datasetSemantic proximity Read

Integrative single-cell analysis by transcriptional and epigenetic states in human adult brainSemantic proximity Read

Strategies for cellular deconvolution in human brain RNA sequencing dataSemantic proximity Read

High cell-type specificity of eQTLs revealed by single-nucleus analyses of brain and bloodSemantic proximity Read

NETSseq Reveals Inflammatory and Aging Mechanisms in Distinct Cell Types Driving Cerebellar Decline in Ataxia TelangiectasiaSemantic proximity Read

Transcriptomic profiling of nuclei from PFA-fixed and FFPE brain tissuesSemantic proximity Read