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Nuclear oligo hashing improves differential analysis of single-cell RNA-seq

Author

Listed:
  • Hyeon-Jin Kim

    (University of Washington)

  • Greg Booth

    (University of Washington)

  • Lauren Saunders

    (University of Washington)

  • Sanjay Srivatsan

    (University of Washington)

  • José L. McFaline-Figueroa

    (Columbia University)

  • Cole Trapnell

    (University of Washington
    Brotman Baty Institute of Precision Medicine
    Allen Discovery Center for Cell Lineage Tracing)

Abstract

Single-cell RNA sequencing (scRNA-seq) offers a high-resolution molecular view into complex tissues, but suffers from high levels of technical noise which frustrates efforts to compare the gene expression programs of different cell types. “Spike-in” RNA standards help control for technical variation in scRNA-seq, but using them with recently developed, ultra-scalable scRNA-seq methods based on combinatorial indexing is not feasible. Here, we describe a simple and cost-effective method for normalizing transcript counts and subtracting technical variability that improves differential expression analysis in scRNA-seq. The method affixes a ladder of synthetic single-stranded DNA oligos to each cell that appears in its RNA-seq library. With improved normalization we explore chemical perturbations with broad or highly specific effects on gene regulation, including RNA pol II elongation, histone deacetylation, and activation of the glucocorticoid receptor. Our methods reveal that inhibiting histone deacetylation prevents cells from executing their canonical program of changes following glucocorticoid stimulation.

Suggested Citation

  • Hyeon-Jin Kim & Greg Booth & Lauren Saunders & Sanjay Srivatsan & José L. McFaline-Figueroa & Cole Trapnell, 2022. "Nuclear oligo hashing improves differential analysis of single-cell RNA-seq," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-30309-4
    DOI: 10.1038/s41467-022-30309-4
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    References listed on IDEAS

    as
    1. Rodoniki Athanasiadou & Benjamin Neymotin & Nathan Brandt & Wei Wang & Lionel Christiaen & David Gresham & Daniel Tranchina, 2019. "A complete statistical model for calibration of RNA-seq counts using external spike-ins and maximum likelihood theory," PLOS Computational Biology, Public Library of Science, vol. 15(3), pages 1-26, March.
    2. Jong Kyoung Kim & Aleksandra A. Kolodziejczyk & Tomislav Ilicic & Sarah A. Teichmann & John C. Marioni, 2015. "Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression," Nature Communications, Nature, vol. 6(1), pages 1-9, December.
    3. Susanne C. van den Brink & Anna Alemany & Vincent van Batenburg & Naomi Moris & Marloes Blotenburg & Judith Vivié & Peter Baillie-Johnson & Jennifer Nichols & Katharina F. Sonnen & Alfonso Martinez Ar, 2020. "Publisher Correction: Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids," Nature, Nature, vol. 579(7799), pages 11-11, March.
    4. Junyue Cao & Malte Spielmann & Xiaojie Qiu & Xingfan Huang & Daniel M. Ibrahim & Andrew J. Hill & Fan Zhang & Stefan Mundlos & Lena Christiansen & Frank J. Steemers & Cole Trapnell & Jay Shendure, 2019. "The single-cell transcriptional landscape of mammalian organogenesis," Nature, Nature, vol. 566(7745), pages 496-502, February.
    5. Susanne C. van den Brink & Anna Alemany & Vincent van Batenburg & Naomi Moris & Marloes Blotenburg & Judith Vivié & Peter Baillie-Johnson & Jennifer Nichols & Katharina F. Sonnen & Alfonso Martinez Ar, 2020. "Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids," Nature, Nature, vol. 582(7812), pages 405-409, June.
    6. Itay Tirosh & Andrew S. Venteicher & Christine Hebert & Leah E. Escalante & Anoop P. Patel & Keren Yizhak & Jonathan M. Fisher & Christopher Rodman & Christopher Mount & Mariella G. Filbin & Cyril Nef, 2016. "Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma," Nature, Nature, vol. 539(7628), pages 309-313, November.
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