Version history

{
  "kind": "infographic",
  "prompt": "The number of SST subtypes has grown dramatically from ~3 morphological types to >100 transcriptomic clusters over 20 years, but the practical taxonomy level may be ~10 supertypes. This comparison reveals how methodological advances and clustering resolution drive apparent diversity, not necessarily biological reality.",
  "provider": "other",
  "raw_fields": {
    "papers": [
      {
        "doi": "10.1523/jneurosci.0661-06.2006",
        "value": "3",
        "method": "transgenic GFP lines + electrophysiology",
        "metric": "Number of SST subtypes identified",
        "cite_key": "Ma2006",
        "condition": "barrel cortex, 2006",
        "study_system": "mouse",
        "value_source_sentence": "By all criteria, there was nearly perfect segregation of X94 and X98 GFP+ neurons, whereas GIN GFP+ neurons exhibited intermediate properties."
      },
      {
        "doi": "10.1038/nn.4216",
        "value": "~8 SST types within 23 GABAergic types",
        "method": "scRNA-seq (SMART-seq)",
        "metric": "Number of SST transcriptomic types",
        "cite_key": "Tasic2016",
        "condition": "visual cortex, 2016",
        "study_system": "mouse",
        "value_source_sentence": "We identify 49 transcriptomic cell types including 23 GABAergic, 19 glutamatergic and seven non-neuronal types."
      },
      {
        "doi": "10.1038/s41586-018-0654-5",
        "value": "multiple SST types within 133 total types",
        "method": "scRNA-seq (SMART-seq v4)",
        "metric": "Number of SST transcriptomic types",
        "cite_key": "Tasic2018",
        "condition": "VISp + ALM, 2018",
        "study_system": "mouse",
        "value_source_sentence": "We define 133 transcriptomic cell types by deep, single-cell RNA sequencing."
      },
      {
        "doi": "10.1016/j.cell.2020.09.057",
        "value": "13",
        "method": "Patch-seq (multimodal)",
        "metric": "Number of SST met-types",
        "cite_key": "Gouwens2020",
        "condition": "visual cortex, 2020",
        "study_system": "mouse",
        "value_source_sentence": "We identify 13 Sst met-types, which is substantially more than described in previous morphological and electrophysiological studies."
      },
      {
        "doi": "10.1016/j.cell.2021.04.021",
        "value": "11 supertypes + Sst Chodl subclass",
        "method": "scRNA-seq (10x + SMART-seq)",
        "metric": "Number of SST supertypes",
        "cite_key": "Yao2021",
        "condition": "whole isocortex + HPF, 2021",
        "study_system": "mouse",
        "value_source_sentence": "The Sst and Pvalb subclasses are divided into 11 and 3 supertypes, respectively."
      },
      {
        "doi": "10.3389/fncir.2024.1436915",
        "value": "~10 supertypes",
        "method": "review of transcriptomic studies",
        "metric": "Recommended practical SST subtype count",
        "cite_key": "Agmon2024",
        "condition": "neocortex, 2024",
        "study_system": "mouse",
        "value_source_sentence": "We suggest that for experimental analysis, the most useful taxonomic level is the subdivision of somatostatin interneurons into ten or so 'supertypes.'"
      }
    ],
    "comparison_id": "sst-subtype-count-across-studies",
    "comparison_name": "Number of SST Interneuron Subtypes Identified Across Major Taxonomy Studies",
    "comparison_type": "timeline",
    "what_it_reveals": "The number of SST subtypes has grown dramatically from ~3 morphological types to >100 transcriptomic clusters over 20 years, but the practical taxonomy level may be ~10 supertypes. This comparison reveals how methodological advances and clustering resolution drive apparent diversity, not necessarily biological reality.",
    "homogeneity_check": {
      "caveats": [
        "Studies used different brain regions (barrel cortex vs visual cortex vs whole isocortex)",
        "Different methods (electrophysiology/morphology vs scRNA-seq vs multimodal Patch-seq) yield different type counts",
        "Clustering resolution dramatically affects the number of types identified",
        "Some studies count 'types' while others count 'supertypes' or 'met-types' which are different taxonomic levels"
      ],
      "comparable": false
    },
    "suggested_plot_type": "grouped bar"
  },
  "section_id": "section_02_evidence_package",
  "source_url": "https://github.com/AllenNeuralDynamics/ComputationalReviewSST/blob/89b7e9787cd90e942b0adb531d549af3ddad30f1/evidence/section_02_evidence_package.json",
  "target_ref": "wiki_page:computationalreviewsst-02",
  "review_repo": "ComputationalReviewSST",
  "section_ref": "wiki_page:computationalreviewsst-02",
  "source_path": "evidence/section_02_evidence_package.json",
  "source_refs": [
    "paper:paper-ed2a7f08ef35",
    "paper:paper-pm-33186530",
    "paper:paper-45d28ae23ca2",
    "paper:paper-pm-30382198",
    "paper:paper-5d546dd2545a",
    "paper:paper-4dfe44516146"
  ],
  "section_title": "Molecular Identity and Transcriptomic Taxonomy",
  "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": "89b7e9787cd90e942b0adb531d549af3ddad30f1",
    "source_repository_url": "https://github.com/AllenNeuralDynamics/ComputationalReviewSST"
  },
  "generation_status": "complete",
  "review_bundle_ref": "analysis_bundle:ab-8466d095488a",
  "origin_url": "https://github.com/AllenNeuralDynamics/ComputationalReviewSST/blob/89b7e9787cd90e942b0adb531d549af3ddad30f1/evidence/section_02_evidence_package.json",
  "commit_sha": "89b7e9787cd90e942b0adb531d549af3ddad30f1",
  "created_by": "persona-jerome-lecoq-gbo-neuroscience",
  "repository_url": "https://github.com/AllenNeuralDynamics/ComputationalReviewSST"
}