Version history

{
  "scope": "developing mouse primary visual cortex (V1) E11.5 to P56",
  "claim_text": "Single-cell and multi-omics atlas of 568,654 transcriptomes plus 200,061 nuclei sampled densely across mouse V1 development (E11.5 to P56) shows that excitatory cell-type diversity emerges through continuous branching of progenitor lineages with branch points temporally controlled, rather than through abrupt fate switches — implying gradual transcriptomic specification of cortical glutamatergic cell types.",
  "raw_fields": {
    "n": 768715,
    "doi": "10.1038/s41586-025-09644-1",
    "claim": "Single-cell and multi-omics atlas of 568,654 transcriptomes plus 200,061 nuclei sampled densely across mouse V1 development (E11.5 to P56) shows that excitatory cell-type diversity emerges through continuous branching of progenitor lineages with branch points temporally controlled, rather than through abrupt fate switches — implying gradual transcriptomic specification of cortical glutamatergic cell types.",
    "cite_key": "Gao2025",
    "evidence": "Single-cell RNA-seq (568,654 cells) and snMultiome (200,061 nuclei) of mouse visual cortex sampled E11.5 → P56, with computational trajectory analysis.",
    "effect_size": "quantitative — 568,654 cells + 200,061 nuclei across embryonic to adult V1; continuous lineage branching",
    "text_access": "fulltext",
    "study_system": "developing mouse primary visual cortex (V1) E11.5 to P56",
    "argument_role": "supporting",
    "replication_status": "single_study",
    "claim_source_sentence": "We computationally reconstructed a transcriptomic developmental trajectory map of all excitatory, inhibitory and non-neuronal cell types in the visual cortex. Branching points that mark the emergence of new cell types at specific developmental ages and molecular signatures of cellular diversification are identified",
    "source_provenance_status": "ok",
    "replication_evidence_dois": [],
    "effect_size_source_sentence": "568,654 high-quality single-cell transcriptomes and a single-nucleus Multiome dataset of 200,061 high-quality nuclei"
  },
  "section_id": "section_07",
  "source_url": "https://github.com/AllenNeuralDynamics/ComputationalReviewRecurrence/blob/79ce062d54a924ce05953ec90aa9d26044d2b48f/evidence/section_07_evidence_package.json",
  "effect_size": "quantitative — 568,654 cells + 200,061 nuclei across embryonic to adult V1; continuous lineage branching",
  "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-b9b3c1c2e42e"
  ],
  "source_span": "We computationally reconstructed a transcriptomic developmental trajectory map of all excitatory, inhibitory and non-neuronal cell types in the visual cortex. Branching points that mark the emergence of new cell types at specific developmental ages and molecular signatures of cellular diversification are identified",
  "study_system": "developing mouse primary visual cortex (V1) E11.5 to P56",
  "evidence_refs": [
    {
      "ref": "paper:paper-b9b3c1c2e42e"
    }
  ],
  "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": "Single-cell RNA-seq (568,654 cells) and snMultiome (200,061 nuclei) of mouse visual cortex sampled E11.5 → P56, with computational trajectory analysis.",
  "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"
}