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- Live5/17/2026, 4:35:28 PM
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{ "kind": "infographic", "prompt": "Successive Allen taxonomy releases redefine 'transcriptomic cell type' at increasingly fine granularity, making cell-type-specific connectivity rules a moving target.", "provider": "other", "raw_fields": { "papers": [ { "n": 1679, "doi": "10.1038/nn.4216", "value": "49", "method": "single-cell RNA-seq (SMART-seq)", "metric": "n_transcriptomic_types_V1", "n_analyzed": "1679", "ci_or_error": "", "text_access": "abstract_only", "n_definition": "single cells profiled by SMART-seq", "scope_region": "single cortical area (VISp)", "study_system": "adult mouse primary visual cortex (V1)", "taxonomic_level": "fine type (t-type)", "scope_population": "all transcriptomically profiled cortical cells", "value_source_sentence": "We identified 49 transcriptomic cell types, including 23 GABAergic, 19 glutamatergic and 7 non-neuronal types.", "experimental_conditions": "Cre-line targeted FACS-sorted cells, SMART-seq" }, { "n": 23822, "doi": "10.1038/s41586-018-0654-5", "value": "133", "method": "single-cell RNA-seq (SMART-seq)", "metric": "n_transcriptomic_types_VISp_ALM", "n_analyzed": "23822", "ci_or_error": "", "text_access": "abstract_only", "n_definition": "single cells profiled by SMART-seq", "scope_region": "two cortical areas", "study_system": "adult mouse primary visual cortex (VISp) and anterior lateral motor cortex (ALM)", "taxonomic_level": "fine type (t-type)", "scope_population": "transcriptomically profiled cortical neurons", "value_source_sentence": "We define 133 transcriptomic cell types by deep, single-cell RNA sequencing.", "experimental_conditions": "Cre-line targeted FACS-sorted cells, SMART-seq" }, { "n": 1300000, "doi": "10.1016/j.cell.2021.04.021", "value": "~1,300,000", "method": "single-cell RNA-seq (10x)", "metric": "n_cells_profiled_isocortex_HPF", "n_analyzed": "1300000", "ci_or_error": "", "text_access": "abstract_only", "n_definition": "single cells profiled by scRNA-seq", "scope_region": "whole isocortex + hippocampal formation", "study_system": "adult mouse isocortex and hippocampal formation", "taxonomic_level": "fine type (t-type)", "scope_population": "all dissociated cells", "value_source_sentence": "We profiled ~1.3 million cells covering the entire adult mouse isocortex and HPF and derived a transcriptomic cell-type taxonomy revealing a comprehensive repertoire of glutamatergic and GABAergic neuron types.", "experimental_conditions": "whole isocortex+HPF dissociation, 10x scRNA-seq" }, { "n": 4000000, "doi": "10.1038/s41586-023-06812-z", "value": "5322", "method": "scRNA-seq + MERFISH", "metric": "n_clusters_whole_brain_atlas", "n_analyzed": "4000000", "ci_or_error": "", "text_access": "abstract_only", "n_definition": "single cells profiled by scRNA-seq post-QC", "scope_region": "whole mouse brain", "study_system": "adult mouse whole brain", "taxonomic_level": "cluster", "scope_population": "all dissociated cells", "value_source_sentence": "The atlas is hierarchically organized into 4 nested levels of classification: 34 classes, 338 subclasses, 1,201 supertypes and 5,322 clusters.", "experimental_conditions": "10x scRNA-seq + MERFISH spatial transcriptomics" } ], "audit_issues": [ { "dimension": "scope_region", "description": "Rows span V1 only → VISp+ALM → whole isocortex+HPF → whole brain. With expanding brain coverage, cluster counts mechanically increase from added regions, not from finer resolution within a fixed scope. This is the canonical scope-mismatch trap.", "entries_affected": [ "10.1038/nn.4216", "10.1038/s41586-018-0654-5", "10.1016/j.cell.2021.04.021", "10.1038/s41586-023-06812-z" ] }, { "dimension": "metric_definition", "description": "Row 3 reports n_cells_profiled (~1,300,000) — a sample-size measure — while rows 1, 2, 4 report n_transcriptomic_types (49, 133, 5,322). These are different quantities on different scales (cells vs. types) and cannot share a y-axis.", "entries_affected": [ "10.1016/j.cell.2021.04.021" ] }, { "dimension": "taxonomic_level", "description": "Rows mix t-types (rows 1–2) with hierarchically-organised 'clusters' (row 4, finest level of a 4-level taxonomy: 34 classes / 338 subclasses / 1,201 supertypes / 5,322 clusters). 5,322 clusters and 49 t-types are not at the same taxonomic grain.", "entries_affected": [ "10.1038/nn.4216", "10.1038/s41586-018-0654-5", "10.1038/s41586-023-06812-z" ] } ], "audit_verdict": "REDESIGN", "comparison_id": "transcriptomic-cell-types-mouse-cortex", "comparison_name": "Number of transcriptomic cell types defined in successive mouse cortex single-cell taxonomies", "comparison_type": "timeline", "what_it_reveals": "Successive Allen taxonomy releases redefine 'transcriptomic cell type' at increasingly fine granularity, making cell-type-specific connectivity rules a moving target.", "homogeneity_check": { "caveats": [ "Each study expands geographic coverage (V1 → VISp+ALM → isocortex+HPF → whole brain), so cluster counts are not directly comparable.", "Taxonomic granularity differs (t-types vs 'supertypes' vs 'clusters')." ], "n_definition_uniform": "true", "scope_region_uniform": "false", "taxonomic_level_uniform": "false", "scope_population_uniform": "true" }, "suggested_plot_type": "timeline", "mandatory_caption_caveats": [ "Brain coverage expands from V1 → 2 cortical areas → isocortex+HPF → whole brain across rows; cluster counts are not directly comparable as a 'discovery progression' because they reflect added tissue, not finer resolution.", "Taxonomic grain differs: rows 1–2 report t-types; row 4 reports 'clusters' at the finest of four nested levels (whole-brain atlas also has 34 classes / 338 subclasses / 1,201 supertypes that are closer in grain to the earlier t-type counts).", "Phase 7 writer: REDESIGN verdict — implement as: Restrict to a single scope (e.g., mouse cortex) and report taxonomic counts at the equivalent level across studies. For the whole-brain atlas (Yao 2023), use the subclass/supertype count rather than the cluster count if comparing to earlier t-type-level papers. Correct the row-3 metric: replace n_ce" ] }, "section_id": "section_07", "source_url": "https://github.com/AllenNeuralDynamics/ComputationalReviewRecurrence/blob/79ce062d54a924ce05953ec90aa9d26044d2b48f/evidence/section_07_evidence_package.json", "target_ref": "wiki_page:computationalreviewrecurrence-07-celltype-motifs", "review_repo": "ComputationalReviewRecurrence", "section_ref": "wiki_page:computationalreviewrecurrence-07-celltype-motifs", "source_path": "evidence/section_07_evidence_package.json", "source_refs": [ "paper:paper-ed2a7f08ef35", "paper:paper-pm-30382198", "paper:paper-4dfe44516146", "paper:1f98e15e-de06-42f7-9da8-1faa69bba835" ], "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" }, "generation_status": "complete", "review_bundle_ref": "analysis_bundle:ab-d9c479db9be9", "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" }