A comparative strategy for single-nucleus and single-cell transcriptomes confirms accuracy in predicted cell-type expression from nuclear RNA View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2017-12

AUTHORS

Blue B. Lake, Simone Codeluppi, Yun C. Yung, Derek Gao, Jerold Chun, Peter V. Kharchenko, Sten Linnarsson, Kun Zhang

ABSTRACT

Significant heterogeneities in gene expression among individual cells are typically interrogated using single whole cell approaches. However, tissues that have highly interconnected processes, such as in the brain, present unique challenges. Single-nucleus RNA sequencing (SNS) has emerged as an alternative method of assessing a cell's transcriptome through the use of isolated nuclei. However, studies directly comparing expression data between nuclei and whole cells are lacking. Here, we have characterized nuclear and whole cell transcriptomes in mouse single neurons and provided a normalization strategy to reduce method-specific differences related to the length of genic regions. We confirmed a high concordance between nuclear and whole cell transcriptomes in the expression of cell type and metabolic modeling markers, but less so for a subset of genes associated with mitochondrial respiration. Therefore, our results indicate that single-nucleus transcriptome sequencing provides an effective means to profile cell type expression dynamics in previously inaccessible tissues. More... »

PAGES

6031

References to SciGraph publications

  • 2014-10. Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex in NATURE BIOTECHNOLOGY
  • 2010-12. A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1 in BMC SYSTEMS BIOLOGY
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  • 2015-07. Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation in NATURE BIOTECHNOLOGY
  • 2005-10. The External RNA Controls Consortium: a progress report in NATURE METHODS
  • 2007-12. Comparison of the contributions of the nuclear and cytoplasmic compartments to global gene expression in human cells in BMC GENOMICS
  • 2011-12. Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain in NATURE STRUCTURAL & MOLECULAR BIOLOGY
  • 2013-12. Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells in NATURE BIOTECHNOLOGY
  • 2016-03. Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis in NATURE METHODS
  • 2016-02-18. Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons in NATURE PROTOCOLS
  • 2016-02. Adult mouse cortical cell taxonomy revealed by single cell transcriptomics in NATURE NEUROSCIENCE
  • 2016-04-19. Nuclear RNA-seq of single neurons reveals molecular signatures of activation in NATURE COMMUNICATIONS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/s41598-017-04426-w

    DOI

    http://dx.doi.org/10.1038/s41598-017-04426-w

    DIMENSIONS

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    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/28729663


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