A scRNA-seq plus MERFISH atlas integrating ~4 million quality-controlled scRNA-…

A scRNA-seq plus MERFISH atlas integrating ~4 million quality-controlled scRNA-seq cells with ~4.3 million MERFISH cells across the adult mouse brain yielded a four-level hierarchy of 34 classes, 338 subclasses, 1,201 supertypes and 5,322 clusters — the standard reference cell taxonomy now invoked in mouse-cortex E→E synthesis work.

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  "claim": "A scRNA-seq plus MERFISH atlas integrating ~4 million quality-controlled scRNA-seq cells with ~4.3 million MERFISH cells across the adult mouse brain yielded a four-level hierarchy of 34 classes, 338 subclasses, 1,201 supertypes and 5,322 clusters — the standard reference cell taxonomy now invoked in mouse-cortex E→E synthesis work.",
  "cite_key": "Yao2023b",
  "evidence": "~4M scRNA-seq + ~4.3M MERFISH cells; 4-level hierarchy with 5,322 clusters; cell-type spatial correspondence systematically analyzed.",
  "effect_size": "34 classes, 338 subclasses, 1,201 supertypes, 5,322 clusters",
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  "study_system": "Whole adult mouse brain (BICCN-affiliated scRNA-seq + MERFISH atlas)",
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  "replication_status": "paired-with-Zhang2023",
  "claim_source_sentence": "The cell-type atlas was created by combining a single-cell RNA-sequencing (scRNA-seq) dataset of around 7 million cells profiled (approximately 4.0 million cells passing quality control), and a spatial transcriptomic dataset of approximately 4.3 million cells using multiplexed error-robust fluorescence in situ hybridization (MERFISH).",
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The cell-type atlas was created by combining a single-cell RNA-sequencing (scRNA-seq) dataset of around 7 million cells profiled (approximately 4.0 million cells passing quality control), and a spatial transcriptomic dataset of approximately 4.3 million cells using multiplexed error-robust fluorescence in situ hybridization (MERFISH).

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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

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