Version history

{
  "kind": "infographic",
  "prompt": "Off-target recombination rates for SST-Cre vary from 5% to 18% depending on cortical layer and area, with layer 5 showing particularly high off-target rates. This directly affects interpretation of SST-Cre-based optogenetic studies.",
  "provider": "other",
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    "papers": [
      {
        "n": 112,
        "doi": "10.3389/fncir.2013.00195",
        "value": "6-10%",
        "method": "whole-cell recordings + immunostaining",
        "metric": "Off-target recombination in PV+/FS interneurons (SST-IRES-Cre)",
        "cite_key": "Hu2013",
        "ci_or_error": "18% (20/112) in layer 5",
        "text_access": "fulltext",
        "n_definition": "RFP-expressing neurons recorded in cortical layer 5",
        "scope_region": "mouse somatosensory cortex",
        "study_system": "mouse somatosensory cortex (SST-IRES-Cre x Ai14)",
        "taxonomic_level": "subclass (PV vs SST)",
        "scope_population": "Cre-labeled neurons",
        "value_source_sentence": "We found, by a lower estimate, 6–10% off-target recombination in FS interneurons in most cortical areas and layers."
      },
      {
        "n": null,
        "doi": "10.1038/ncomms13664",
        "value": "~95% (5% PV+ off-target cited from Pfeffer et al.)",
        "method": "immunohistochemistry",
        "metric": "Assumed SST-Cre specificity",
        "cite_key": "Walker2016",
        "ci_or_error": null,
        "text_access": "fulltext",
        "n_definition": null,
        "scope_region": "mouse visual cortex",
        "study_system": "mouse visual cortex",
        "taxonomic_level": "subclass",
        "scope_population": "SST-Cre labeled neurons",
        "value_source_sentence": "Most studies using the SOM-Cre line appear to use it without validation; an exception is a recent study that tested recombination specificity and found that 5% of recombined neurons in the visual cortex were immunopositive for PV (Pfeffer et al., 201"
      }
    ],
    "comparison_id": "fig_sec3_cre_specificity",
    "comparison_name": "Off-target recombination rates in SST-Cre lines across studies",
    "comparison_type": "cross-study conflict",
    "what_it_reveals": "Off-target recombination rates for SST-Cre vary from 5% to 18% depending on cortical layer and area, with layer 5 showing particularly high off-target rates. This directly affects interpretation of SST-Cre-based optogenetic studies.",
    "homogeneity_check": "Both studies examine SST-IRES-Cre off-target rates but in different cortical areas (somatosensory vs visual) and using different methods (electrophysiology vs immunostaining). Layer-specific rates are not directly comparable. The 5% estimate from visual cortex uses immunostaining which may undercount PV+ cells with low PV expression.",
    "suggested_plot_type": "dot_with_range"
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  "section_title": "Molecular and Transcriptomic Classification",
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