Version history

{
  "scope": "Whole adult mouse brain (BICCN-affiliated scRNA-seq + MERFISH atlas)",
  "claim_text": "A scRNA-seq plus MERFISH atlas integrating ~4 million quality-controlled scRNA-seq cells with ~4.3 million MERFISH cells across the adult mouse brain yielded a four-level hierarchy of 34 classes, 338 subclasses, 1,201 supertypes and 5,322 clusters — the standard reference cell taxonomy now invoked in mouse-cortex E→E synthesis work.",
  "raw_fields": {
    "n": 4000000,
    "doi": "10.1038/s41586-023-06812-z",
    "claim": "A scRNA-seq plus MERFISH atlas integrating ~4 million quality-controlled scRNA-seq cells with ~4.3 million MERFISH cells across the adult mouse brain yielded a four-level hierarchy of 34 classes, 338 subclasses, 1,201 supertypes and 5,322 clusters — the standard reference cell taxonomy now invoked in mouse-cortex E→E synthesis work.",
    "cite_key": "Yao2023b",
    "evidence": "~4M scRNA-seq + ~4.3M MERFISH cells; 4-level hierarchy with 5,322 clusters; cell-type spatial correspondence systematically analyzed.",
    "effect_size": "34 classes, 338 subclasses, 1,201 supertypes, 5,322 clusters",
    "text_access": "fulltext",
    "study_system": "Whole adult mouse brain (BICCN-affiliated scRNA-seq + MERFISH atlas)",
    "argument_role": "supporting",
    "replication_status": "paired-with-Zhang2023",
    "claim_source_sentence": "The cell-type atlas was created by combining a single-cell RNA-sequencing (scRNA-seq) dataset of around 7 million cells profiled (approximately 4.0 million cells passing quality control), and a spatial transcriptomic dataset of approximately 4.3 million cells using multiplexed error-robust fluorescence in situ hybridization (MERFISH).",
    "source_provenance_status": "ok",
    "replication_evidence_dois": [
      "10.1038/s41586-023-06808-9"
    ],
    "effect_size_source_sentence": "The atlas is hierarchically organized into 4 nested levels of classification: 34 classes, 338 subclasses, 1,201 supertypes and 5,322 clusters."
  },
  "section_id": "section_15",
  "source_url": "https://github.com/AllenNeuralDynamics/ComputationalReviewRecurrence/blob/79ce062d54a924ce05953ec90aa9d26044d2b48f/evidence/section_15_evidence_package.json",
  "effect_size": "34 classes, 338 subclasses, 1,201 supertypes, 5,322 clusters",
  "review_repo": "ComputationalReviewRecurrence",
  "section_ref": "wiki_page:computationalreviewrecurrence-15-methods-limits",
  "source_kind": "review_finding",
  "source_path": "evidence/section_15_evidence_package.json",
  "source_refs": [
    "paper:1f98e15e-de06-42f7-9da8-1faa69bba835"
  ],
  "source_span": "The cell-type atlas was created by combining a single-cell RNA-sequencing (scRNA-seq) dataset of around 7 million cells profiled (approximately 4.0 million cells passing quality control), and a spatial transcriptomic dataset of approximately 4.3 million cells using multiplexed error-robust fluorescence in situ hybridization (MERFISH).",
  "study_system": "Whole adult mouse brain (BICCN-affiliated scRNA-seq + MERFISH atlas)",
  "evidence_refs": [
    {
      "ref": "paper:1f98e15e-de06-42f7-9da8-1faa69bba835"
    }
  ],
  "section_title": "15. Methodological limits and emerging tools — what current mouse-cortex tools cannot yet measure about E→E recurrence (subthreshold network activity, fast plasticity in vivo, millimetre-scale dynamic connectomes), and what is on the near horizon",
  "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": "~4M scRNA-seq + ~4.3M MERFISH cells; 4-level hierarchy with 5,322 clusters; cell-type spatial correspondence systematically analyzed.",
  "review_bundle_ref": "analysis_bundle:ab-d9c479db9be9",
  "replication_status": "paired-with-Zhang2023",
  "review_package_ref": "analysis_bundle:ab-d9c479db9be9",
  "source_artifact_ref": "wiki_page:computationalreviewrecurrence-15-methods-limits",
  "origin_url": "https://github.com/AllenNeuralDynamics/ComputationalReviewRecurrence/blob/79ce062d54a924ce05953ec90aa9d26044d2b48f/evidence/section_15_evidence_package.json",
  "commit_sha": "79ce062d54a924ce05953ec90aa9d26044d2b48f",
  "created_by": "persona-jerome-lecoq-gbo-neuroscience",
  "repository_url": "https://github.com/AllenNeuralDynamics/ComputationalReviewRecurrence"
}