Rxivist logo

Transcriptional profiling of complex tissues by RNA-sequencing of single nuclei presents some advantages over whole cell analysis. It enables unbiased cellular coverage, lack of cell isolation-based transcriptional effects, and application to archived frozen specimens. Using a well-matched pair of single-nucleus RNA-seq (snRNA-seq) and single-cell RNA-seq (scRNA-seq) SMART-Seq v4 datasets from mouse visual cortex, we demonstrate that similarly high-resolution clustering of closely related neuronal types can be achieved with both methods if intronic sequences are included in nuclear RNA-seq analysis. More transcripts are detected in individual whole cells (~11,000 genes) than nuclei (~7,000 genes), but the majority of genes have similar detection across cells and nuclei. We estimate that the nuclear proportion of total cellular mRNA varies from 20% to over 50% for large and small pyramidal neurons, respectively. Together, these results illustrate the high information content of nuclear RNA for characterization of cellular diversity in brain tissues.

Download data

  • Downloaded 4,083 times
  • Download rankings, all-time:
    • Site-wide: 4,164
    • In neuroscience: 288
  • Year to date:
    • Site-wide: 54,785
  • Since beginning of last month:
    • Site-wide: 43,031

Altmetric data

Downloads over time

Distribution of downloads per paper, site-wide