SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data

GigaScience, Journal Year: 2020, Volume and Issue: 9(12)

Published: Dec. 1, 2020

Abstract Background Droplet-based single-cell RNA sequence analyses assume that all acquired RNAs are endogenous to cells. However, any cell-free contained within the input solution also captured by these assays. This sequencing of constitutes a background contamination confounds biological interpretation transcriptomic data. Results We demonstrate from this "soup" is ubiquitous, with experiment-specific variations in composition and magnitude. present method, SoupX, for quantifying extent estimating "background-corrected" cell expression profiles seamlessly integrate existing downstream analysis tools. Applying method several datasets using multiple droplet technologies, we its application improves otherwise misleading data, as well improving quality control metrics. Conclusions tool removing ambient droplet-based experiments. has broad applicability, can improve utility future datasets.

Language: Английский

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COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets

Nature, Journal Year: 2021, Volume and Issue: 595(7865), P. 107 - 113

Published: April 29, 2021

Language: Английский

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A molecular single-cell lung atlas of lethal COVID-19

Nature, Journal Year: 2021, Volume and Issue: 595(7865), P. 114 - 119

Published: April 29, 2021

Language: Английский

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Best practices for single-cell analysis across modalities

Nature Reviews Genetics, Journal Year: 2023, Volume and Issue: 24(8), P. 550 - 572

Published: March 31, 2023

Language: Английский

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A single-cell atlas of human and mouse white adipose tissue

Nature, Journal Year: 2022, Volume and Issue: 603(7903), P. 926 - 933

Published: March 16, 2022

Language: Английский

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Transcriptional and Cellular Diversity of the Human Heart

Circulation, Journal Year: 2020, Volume and Issue: 142(5), P. 466 - 482

Published: May 14, 2020

The human heart requires a complex ensemble of specialized cell types to perform its essential function. A greater knowledge the intricate cellular milieu is critical increase our understanding cardiac homeostasis and pathology. As recent advances in low-input RNA sequencing have allowed definitions transcriptomes at single-cell resolution scale, we applied these approaches assess transcriptional diversity nonfailing heart.

Language: Английский

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Joint probabilistic modeling of single-cell multi-omic data with totalVI

Nature Methods, Journal Year: 2021, Volume and Issue: 18(3), P. 272 - 282

Published: Feb. 15, 2021

Language: Английский

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Molecular logic of cellular diversification in the mouse cerebral cortex

Nature, Journal Year: 2021, Volume and Issue: 595(7868), P. 554 - 559

Published: June 23, 2021

Language: Английский

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snRNA-seq reveals a subpopulation of adipocytes that regulates thermogenesis

Nature, Journal Year: 2020, Volume and Issue: 587(7832), P. 98 - 102

Published: Oct. 28, 2020

Language: Английский

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Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19

Cell, Journal Year: 2021, Volume and Issue: 184(18), P. 4713 - 4733.e22

Published: July 23, 2021

SARS-CoV-2 infection can cause severe respiratory COVID-19. However, many individuals present with isolated upper symptoms, suggesting potential to constrain viral pathology the nasopharynx. Which cells primarily targets and how influences epithelium remains incompletely understood. We performed scRNA-seq on nasopharyngeal swabs from 58 healthy COVID-19 participants. During COVID-19, we observe expansion of secretory, loss ciliated, epithelial cell repopulation via deuterosomal expansion. In mild moderate express anti-viral/interferon-responsive genes, while in have muted anti-viral responses despite equivalent loads. RNA

Language: Английский

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