Version history

{
  "scope": "Mouse visual cortex; developmental scRNA-seq + snMultiome atlas",
  "claim_text": "A developmental transcriptomic and epigenomic atlas of mouse visual cortex built from 568,654 scRNA-seq cells and 200,061 multiome nuclei reveals continuous, staggered emergence of cortical cell types, including late emergence during the critical-period onset — demonstrating that single-snapshot Patch-seq taxonomies miss developmentally derived structure.",
  "raw_fields": {
    "n": 568654,
    "doi": "10.1038/s41586-025-09644-1",
    "claim": "A developmental transcriptomic and epigenomic atlas of mouse visual cortex built from 568,654 scRNA-seq cells and 200,061 multiome nuclei reveals continuous, staggered emergence of cortical cell types, including late emergence during the critical-period onset — demonstrating that single-snapshot Patch-seq taxonomies miss developmentally derived structure.",
    "cite_key": "Gao2025",
    "evidence": "Sets the present-day scale of mouse-cortex transcriptomic profiling and highlights what is missed without dense temporal sampling — relevant to cluster_14's outlook for large-scale Patch-seq.",
    "effect_size": "568,654 single-cell transcriptomes; 200,061 multiome nuclei; E11.5 to P56",
    "text_access": "abstract_only",
    "study_system": "Mouse visual cortex; developmental scRNA-seq + snMultiome atlas",
    "argument_role": "supporting",
    "replication_status": "single-study",
    "claim_source_sentence": "The atlas is built from a single-cell RNA sequencing dataset of 568,654 high-quality single-cell transcriptomes and a single-nucleus Multiome dataset of 200,061 high-quality nuclei, which were densely sampled across the embryonic and postnatal developmental stages (from embryonic day 11.5 to postnatal day 56).",
    "source_provenance_status": "non_substring_match",
    "replication_evidence_dois": [],
    "effect_size_source_sentence": "The atlas is built from a single-cell RNA sequencing dataset of 568,654 high-quality single-cell transcriptomes and a single-nucleus Multiome dataset of 200,061 high-quality nuclei, which were densely sampled across the embryonic and postnatal developmental stages (from embryonic day 11.5 to postnatal day 56)."
  },
  "section_id": "section_15",
  "source_url": "https://github.com/AllenNeuralDynamics/ComputationalReviewRecurrence/blob/79ce062d54a924ce05953ec90aa9d26044d2b48f/evidence/section_15_evidence_package.json",
  "effect_size": "568,654 single-cell transcriptomes; 200,061 multiome nuclei; E11.5 to P56",
  "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:paper-b9b3c1c2e42e"
  ],
  "source_span": "The atlas is built from a single-cell RNA sequencing dataset of 568,654 high-quality single-cell transcriptomes and a single-nucleus Multiome dataset of 200,061 high-quality nuclei, which were densely sampled across the embryonic and postnatal developmental stages (from embryonic day 11.5 to postnatal day 56).",
  "study_system": "Mouse visual cortex; developmental scRNA-seq + snMultiome atlas",
  "evidence_refs": [
    {
      "ref": "paper:paper-b9b3c1c2e42e"
    }
  ],
  "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": "Sets the present-day scale of mouse-cortex transcriptomic profiling and highlights what is missed without dense temporal sampling — relevant to cluster_14's outlook for large-scale Patch-seq.",
  "review_bundle_ref": "analysis_bundle:ab-d9c479db9be9",
  "replication_status": "single-study",
  "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"
}