A 1.3-million-cell scRNA-seq taxonomy of adult mouse isocortex and hippocampal…

A 1.3-million-cell scRNA-seq taxonomy of adult mouse isocortex and hippocampal formation organizes GABAergic interneurons into two developmental-origin neighborhoods (CGE and MGE), with the CGE neighborhood divided into Lamp5, Sncg and Vip subclasses (4, 5, and 6 supertypes respectively) and the MGE neighborhood into Sst Chodl, Sst, and Pvalb (1, 11, and 3 supertypes); identifies six Vip supertypes as the developmentally CGE-derived Vip lineage backbone.

{
  "n": 1300000,
  "doi": "10.1016/j.cell.2021.04.021",
  "claim": "A 1.3-million-cell scRNA-seq taxonomy of adult mouse isocortex and hippocampal formation organizes GABAergic interneurons into two developmental-origin neighborhoods (CGE and MGE), with the CGE neighborhood divided into Lamp5, Sncg and Vip subclasses (4, 5, and 6 supertypes respectively) and the MGE neighborhood into Sst Chodl, Sst, and Pvalb (1, 11, and 3 supertypes); identifies six Vip supertypes as the developmentally CGE-derived Vip lineage backbone.",
  "title": null,
  "cite_key": "Yao2021a",
  "evidence": "~1.3 million cells from entire adult mouse isocortex and HPF profiled by 10x scRNA-seq; integrated UMAP and hierarchical clustering; supertype/subclass nomenclature.",
  "effect_size": "6 Vip supertypes (CGE), 5 Sncg supertypes, 4 Lamp5 supertypes",
  "figure_data": [
    {
      "type": "cell_type_count",
      "unit": "supertypes",
      "value": 6,
      "metric": "Number of CGE Vip supertypes in mouse cortex+HPF",
      "source": "Yao 2021 Fig. 2D / Table S3",
      "context": "out of 1.3M cells; CGE neighborhood = Lamp5/Sncg/Vip"
    }
  ],
  "text_access": "fulltext",
  "study_system": "mouse, isocortex + HPF (adult, scRNA-seq)",
  "_source_cluster": "cluster_02_development_lineage",
  "replication_status": "primary",
  "_source_cluster_index": 103,
  "claim_source_sentence": "GABAergic cell type taxonomy The GABAergic inhibitory neuronal class is divided into two neighborhoods that correlate with distinct developmental origins: caudal ganglionic eminence (CGE) ( Fig. 2A – E ) and medial ganglionic eminence (MGE) ( Fig. 2F – J ). Each neighborhood is further divided into 3 subclasses: Lamp5, Sncg and Vip in CGE, and Sst Chodl, Sst and Pvalb in MGE. In the CGE neighborhood, the Lamp5 (mostly neurogliaform cells), Sncg and Vip subclasses are divided into 4, 5 (one containing Vip cells), and 6 supertypes, respectively ( Fig. 2D , Table S3 ).",
  "replication_evidence_dois": [
    "10.1038/s41586-018-0654-5"
  ],
  "effect_size_source_sentence": "In the CGE neighborhood, the Lamp5 (mostly neurogliaform cells), Sncg and Vip subclasses are divided into 4, 5 (one containing Vip cells), and 6 supertypes, respectively ( Fig. 2D , Table S3 )."
}

[
  "paper:paper-4dfe44516146"
]

GABAergic cell type taxonomy The GABAergic inhibitory neuronal class is divided into two neighborhoods that correlate with distinct developmental origins: caudal ganglionic eminence (CGE) ( Fig. 2A – E ) and medial ganglionic eminence (MGE) ( Fig. 2F – J ). Each neighborhood is further divided into 3 subclasses: Lamp5, Sncg and Vip in CGE, and Sst Chodl, Sst and Pvalb in MGE. In the CGE neighborhood, the Lamp5 (most...

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  "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."
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  "source_commit_sha": "95e761177f7d2ec565983d3307c14ec238f9677c",
  "source_repository_url": "https://github.com/AllenNeuralDynamics/ComputationalReviewVIP"
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