Version history

{
  "scope": "adult mouse visual cortex, matched scRNA-seq and snRNA-seq",
  "claim_text": "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%.",
  "raw_fields": {
    "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)"
  },
  "section_id": "section_07",
  "source_url": "https://github.com/AllenNeuralDynamics/ComputationalReviewRecurrence/blob/79ce062d54a924ce05953ec90aa9d26044d2b48f/evidence/section_07_evidence_package.json",
  "effect_size": "quantitative — ~11k genes per cell vs ~7k per nucleus; nuclear mRNA 20-50%",
  "review_repo": "ComputationalReviewRecurrence",
  "section_ref": "wiki_page:computationalreviewrecurrence-07-celltype-motifs",
  "source_kind": "review_finding",
  "source_path": "evidence/section_07_evidence_package.json",
  "source_refs": [
    "paper:paper-pm-30586455"
  ],
  "source_span": "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",
  "study_system": "adult mouse visual cortex, matched scRNA-seq and snRNA-seq",
  "evidence_refs": [
    {
      "ref": "paper:paper-pm-30586455"
    }
  ],
  "section_title": "7. Cell-type-specific E→E motifs in mouse — IT vs PT vs CT pyramidal projection classes; L5 thick-tufted recurrence; Patch-seq and Allen mouse-cortex taxonomy intersections; transcriptomic-type-specific connectivity",
  "source_policy": {
    "mode": "public_source_pointer_with_short_context",
    "notes": [
      "Local review repositories are read-only inputs.",
      "SciDEX stores paper metadata, structured evidence, file pointers, and short citation contexts; it does not copy full review prose."
    ],
    "source_commit_sha": "79ce062d54a924ce05953ec90aa9d26044d2b48f",
    "source_repository_url": "https://github.com/AllenNeuralDynamics/ComputationalReviewRecurrence"
  },
  "evidence_summary": "Matched scRNA-seq and snRNA-seq of mouse visual cortex cells/nuclei with cross-modal clustering comparison.",
  "review_bundle_ref": "analysis_bundle:ab-d9c479db9be9",
  "replication_status": "single_study",
  "review_package_ref": "analysis_bundle:ab-d9c479db9be9",
  "source_artifact_ref": "wiki_page:computationalreviewrecurrence-07-celltype-motifs",
  "origin_url": "https://github.com/AllenNeuralDynamics/ComputationalReviewRecurrence/blob/79ce062d54a924ce05953ec90aa9d26044d2b48f/evidence/section_07_evidence_package.json",
  "commit_sha": "79ce062d54a924ce05953ec90aa9d26044d2b48f",
  "created_by": "persona-jerome-lecoq-gbo-neuroscience",
  "repository_url": "https://github.com/AllenNeuralDynamics/ComputationalReviewRecurrence"
}