Comparison of matched single-nucleus and single-cell RNA-seq datasets from mous…

Comparison of matched single-nucleus and single-cell RNA-seq datasets from mouse visual cortex shows that closely related neuronal types can be similarly discriminated by both methods if intronic reads are included in snRNA-seq analysis, with ~11,000 genes detected per cell vs ~7,000 per nucleus and large-pyramid nuclear-mRNA fractions estimated at 20-50%.

{
  "n": 0,
  "doi": "10.1371/journal.pone.0209648",
  "claim": "Comparison of matched single-nucleus and single-cell RNA-seq datasets from mouse visual cortex shows that closely related neuronal types can be similarly discriminated by both methods if intronic reads are included in snRNA-seq analysis, with ~11,000 genes detected per cell vs ~7,000 per nucleus and large-pyramid nuclear-mRNA fractions estimated at 20-50%.",
  "cite_key": "Bakken2018",
  "evidence": "Matched scRNA-seq and snRNA-seq of mouse visual cortex cells/nuclei with cross-modal clustering comparison.",
  "effect_size": "quantitative — ~11k genes per cell vs ~7k per nucleus; nuclear mRNA 20-50%",
  "text_access": "fulltext",
  "study_system": "adult mouse visual cortex, matched scRNA-seq and snRNA-seq",
  "argument_role": "supporting",
  "replication_status": "single_study",
  "claim_source_sentence": "Although more transcripts are detected in individual whole cells (~11,000 genes) than nuclei (~7,000 genes), we demonstrate that closely related neuronal cell types can be similarly discriminated with both methods if intronic sequences are included in snRNA-seq analysis. We estimate that the nuclear proportion of total cellular mRNA varies from 20% to over 50% for large and small pyramidal neurons, respectively",
  "source_provenance_status": "ok",
  "replication_evidence_dois": [],
  "effect_size_source_sentence": "~11,000 genes [per cell] than nuclei (~7,000 genes)"
}

[
  "paper:paper-pm-30586455"
]

Although more transcripts are detected in individual whole cells (~11,000 genes) than nuclei (~7,000 genes), we demonstrate that closely related neuronal cell types can be similarly discriminated with both methods if intronic sequences are included in snRNA-seq analysis. We estimate that the nuclear proportion of total cellular mRNA varies from 20% to over 50% for large and small pyramidal neurons, respectively

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