核糖核酸
生物
生物信息学
污染
小核RNA
RNA序列
RNA编辑
细胞
转录组
基因表达
基因
非编码RNA
生物化学
生态学
作者
Emre Caglayan,Yuxiang Liu,Genevieve Konopka
出处
期刊:Neuron
[Elsevier]
日期:2022-12-01
卷期号:110 (24): 4043-4056.e5
被引量:23
标识
DOI:10.1016/j.neuron.2022.09.010
摘要
Ambient RNA contamination in single-cell and single-nuclei RNA sequencing (snRNA-seq) is a significant problem, but its consequences are poorly understood. Here, we show that ambient RNAs in brain snRNA-seq datasets have a nuclear or non-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 ambient RNA contamination. We detect pervasive neuronal ambient RNA contamination in all glial cell types unless glia and neurons are physically separated prior to sequencing. We demonstrate that this contamination can be removed in silico and show that previous single-nuclei RNA-seq-based annotations of immature oligodendrocytes are glial nuclei contaminated with ambient RNAs. After ambient RNA removal, we detect rare, committed oligodendrocyte progenitor cells not annotated in most previous adult human brain datasets. Together, these results provide an in-depth analysis of ambient RNA contamination in brain single-nuclei datasets.
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