SPIDER-Seq integrates viral-barcoded retrograde tracing with single-cell sequen…

SPIDER-Seq integrates viral-barcoded retrograde tracing with single-cell sequencing and spatial omics to produce an integrated single-cell projectome–transcriptome–anatomy atlas of mouse prefrontal cortex, identifying gradient spatial occupation of projection neurons and predicting individual neuron projection targets from gene expression with high accuracy.

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  "doi": "10.1093/nsr/nwag004",
  "claim": "SPIDER-Seq integrates viral-barcoded retrograde tracing with single-cell sequencing and spatial omics to produce an integrated single-cell projectome–transcriptome–anatomy atlas of mouse prefrontal cortex, identifying gradient spatial occupation of projection neurons and predicting individual neuron projection targets from gene expression with high accuracy.",
  "cite_key": "Sun2026",
  "evidence": "Integrated projectome + scRNA-seq + spatial omics in mouse PFC; ML-based per-neuron projection prediction; demonstrated on fear-recall engram neurons.",
  "effect_size": "machine-learning predicted neuron projections from gene profile + spatial info; applied to fear-recall engram neurons",
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  "study_system": "Mouse PFC (SPIDER-Seq integrated atlas)",
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  "replication_status": "single-study",
  "claim_source_sentence": "We developed a Single-cell Projectome-transcriptome In situ Deciphering Sequencing (SPIDER-Seq) technique by combining viral barcoding tracing with single-cell sequencing and spatial-omics. This empowers us to delineate an integrated single-cell spatial molecular, cellular, anatomic and projectomic atlas of the mouse prefrontal cortex (PFC).",
  "source_provenance_status": "ok",
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  "effect_size_source_sentence": "leveraging machine learning, we predicted neuron projections with high accuracy by combining gene profiles and spatial information."
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We developed a Single-cell Projectome-transcriptome In situ Deciphering Sequencing (SPIDER-Seq) technique by combining viral barcoding tracing with single-cell sequencing and spatial-omics. This empowers us to delineate an integrated single-cell spatial molecular, cellular, anatomic and projectomic atlas of the mouse prefrontal cortex (PFC).

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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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