Dissecting Cell-Type Composition and Activity-Dependent Transcriptional State in Mammalian Brains by Massively Parallel Single-Nucleus RNA-Seq

Mol Cell. 2017 Dec 7;68(5):1006-1015.e7. doi: 10.1016/j.molcel.2017.11.017.


Massively parallel single-cell RNA sequencing can precisely resolve cellular diversity in a high-throughput manner at low cost, but unbiased isolation of intact single cells from complex tissues such as adult mammalian brains is challenging. Here, we integrate sucrose-gradient-assisted purification of nuclei with droplet microfluidics to develop a highly scalable single-nucleus RNA-seq approach (sNucDrop-seq), which is free of enzymatic dissociation and nucleus sorting. By profiling ∼18,000 nuclei isolated from cortical tissues of adult mice, we demonstrate that sNucDrop-seq not only accurately reveals neuronal and non-neuronal subtype composition with high sensitivity but also enables in-depth analysis of transient transcriptional states driven by neuronal activity, at single-cell resolution, in vivo.

Keywords: Single-nucleus RNA-seq; cell type classification; cerebral cortex; droplet microfludics; neuronal-activity-induced transcription; sNucDrop-seq; seizure; single-cell transcriptomics.

MeSH terms

  • Animals
  • Cell Nucleus / metabolism*
  • Cell Nucleus / pathology
  • Centrifugation, Density Gradient
  • Cerebral Cortex / metabolism*
  • Cerebral Cortex / pathology
  • Cerebral Cortex / physiopathology
  • Disease Models, Animal
  • High-Throughput Nucleotide Sequencing*
  • Human Embryonic Stem Cells / metabolism
  • Humans
  • Kinetics
  • Male
  • Mice
  • Mice, Inbred C57BL
  • Microfluidic Analytical Techniques
  • NIH 3T3 Cells
  • Neural Inhibition
  • Neurons / metabolism*
  • Neurons / pathology
  • Pentylenetetrazole
  • RNA / genetics*
  • RNA / metabolism
  • Seizures / genetics*
  • Seizures / metabolism
  • Seizures / pathology
  • Seizures / physiopathology
  • Sequence Analysis, RNA / methods*
  • Single-Cell Analysis / methods*
  • Synaptic Transmission
  • Transcription, Genetic*
  • Transfection


  • RNA
  • Pentylenetetrazole