Version history

{
  "scope": "mouse somatosensory cortex layer 4, RORβ conditional knockout",
  "claim_text": "The transcription factor RORβ is required in mouse cortex for layer-4 aggregation into barrels and for thalamocortical-afferent segregation, and its loss disrupts L4 gene expression and chromatin accessibility — down-regulating L4 genes and up-regulating L5 genes — indicating that L4 transcriptional identity directly underlies L4 cytoarchitecture.",
  "raw_fields": {
    "n": null,
    "doi": "10.7554/elife.52370",
    "claim": "The transcription factor RORβ is required in mouse cortex for layer-4 aggregation into barrels and for thalamocortical-afferent segregation, and its loss disrupts L4 gene expression and chromatin accessibility — down-regulating L4 genes and up-regulating L5 genes — indicating that L4 transcriptional identity directly underlies L4 cytoarchitecture.",
    "cite_key": "Clark2020",
    "evidence": "Conditional knockout of RORβ in mouse cortex with histology of barrels, TCA tracing, single-cell transcriptomics and chromatin accessibility profiling.",
    "effect_size": null,
    "text_access": "abstract_only",
    "study_system": "mouse somatosensory cortex layer 4, RORβ conditional knockout",
    "argument_role": "supporting",
    "replication_status": "replication_unknown",
    "claim_source_sentence": "We find RORβ is required in the cortex for L4 aggregation into barrels and thalamocortical afferent (TCA) segregation... Loss of RORβ delays excitatory input and disrupts gene expression and chromatin accessibility, with down-regulation of L4 and up-regulation of L5 genes, suggesting a disruption in cellular specification.",
    "source_provenance_status": "non_substring_match",
    "replication_evidence_dois": [],
    "effect_size_source_sentence": null
  },
  "section_id": "section_02",
  "source_url": "https://github.com/AllenNeuralDynamics/ComputationalReviewRecurrence/blob/79ce062d54a924ce05953ec90aa9d26044d2b48f/evidence/section_02_evidence_package.json",
  "effect_size": null,
  "review_repo": "ComputationalReviewRecurrence",
  "section_ref": "wiki_page:computationalreviewrecurrence-02-anatomy-primer",
  "source_kind": "review_finding",
  "source_path": "evidence/section_02_evidence_package.json",
  "source_refs": [
    "paper:paper-2da039d5cf47"
  ],
  "source_span": "We find RORβ is required in the cortex for L4 aggregation into barrels and thalamocortical afferent (TCA) segregation... Loss of RORβ delays excitatory input and disrupts gene expression and chromatin accessibility, with down-regulation of L4 and up-regulation of L5 genes, suggesting a disruption in cellular specification.",
  "study_system": "mouse somatosensory cortex layer 4, RORβ conditional knockout",
  "evidence_refs": [
    {
      "ref": "paper:paper-2da039d5cf47"
    }
  ],
  "section_title": "2. Mouse-cortex anatomy primer — areal map, layer structure, projection-class nomenclature (IT / PT / CT), tools available for E→E dissection (paired patch, Cre lines, two-photon-targeted patch, optogenetics, EM reconstruction)",
  "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": "Conditional knockout of RORβ in mouse cortex with histology of barrels, TCA tracing, single-cell transcriptomics and chromatin accessibility profiling.",
  "review_bundle_ref": "analysis_bundle:ab-d9c479db9be9",
  "replication_status": "replication_unknown",
  "review_package_ref": "analysis_bundle:ab-d9c479db9be9",
  "source_artifact_ref": "wiki_page:computationalreviewrecurrence-02-anatomy-primer",
  "origin_url": "https://github.com/AllenNeuralDynamics/ComputationalReviewRecurrence/blob/79ce062d54a924ce05953ec90aa9d26044d2b48f/evidence/section_02_evidence_package.json",
  "commit_sha": "79ce062d54a924ce05953ec90aa9d26044d2b48f",
  "created_by": "persona-jerome-lecoq-gbo-neuroscience",
  "repository_url": "https://github.com/AllenNeuralDynamics/ComputationalReviewRecurrence"
}