Cited by 580Neuroscience and Neuropharmacology ResearchSingle-cell and spatial transcriptomicsNeural dynamics and brain function

Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells

Open access
Gouwens, Nathan W., Sorensen, Staci A., Baftizadeh, Fahimeh, Budzillo, Agata, Lee, Brian R., Jarsky, Tim, Alfiler, Lauren, Baker, Katherine +90 more·2020·Cell

Published version of a preprint

Abstract

Neurons are frequently classified into distinct types on the basis of structural, physiological, or genetic attributes. To better constrain the definition of neuronal cell types, we characterized the transcriptomes and intrinsic physiological properties of over 4,200 mouse visual cortical GABAergic interneurons and reconstructed the local morphologies of 517 of those neurons. We find that most transcriptomic types (t-types) occupy specific laminar positions within visual cortex, and, for most types, the cells mapping to a t-type exhibit consistent electrophysiological and morphological properties. These properties display both discrete and continuous variation among t-types. Through multimodal integrated analysis we define 28 met-types that have congruent morphological, electrophysiological, and transcriptomic properties and robust mutual predictability. We identify layer-specific axon innervation pattern as a defining feature distinguishing different met-types. These met-types represent a unified definition of cortical GABAergic interneuron types, providing a systematic framework to capture existing knowledge and bridge future analyses across different modalities.

Integrity signals

Registry

Crossref · 10.1016/j.cell.2020.09.057

Cites

92 of 92 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 53 cited sources checked · 0 supported · 0 flagged

  • Findingown data

    For most t-types, the cells mapping to a t-type exhibit consistent electrophysiological and morphological properties.

    “for most types, the cells mapping to a t-type exhibit consistent electrophysiological and morphological properties”
    Quote in the paperSubstantial claim
  • Findingown data

    Most transcriptomic types (t-types) occupy specific laminar positions within visual cortex.

    “We find that most transcriptomic types (t-types) occupy specific laminar positions within visual cortex”
    Quote in the paperSubstantial claim
  • Findingcitation

    mRNA collected from one neuron via Patch-seq often includes contaminating mRNA from adjacent neurons and/or non-neuronal cells.

    “we (Figure S2B) and others (Tripathy et al., 2018) found that the mRNA collected from one neuron via a Patch-seq recording often includes contaminating mRNA from adjacent neurons and/or non-neuronal cells.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Tripathy et al., 2018 source

      Not checked in the free run.

  • Findingown data

    The scRNAseq transcriptomes from Patch-seq recordings exhibited a similar number of total genes as those from dissociated neurons.

    “The scRNAseq transcriptomes from cDNA obtained from Patch-seq recordings of individual GABAergic interneurons exhibited a similar number of total genes as the scRNAseq transcriptomes obtained from individual dissociated neurons”
    Quote in the paperSubstantial claim
  • Findingown data

    The two transcriptomic datasets had similar structure when visualized together via UMAP.

    “the two transcriptomic datasets had similar structure when visualized together via a Uniform Manifold Approximation and Projection (UMAP, (Becht et al., 2018)) method”
    Quote in the paperSubstantial claim
  • May combine two claims. 52
  • The quote only partly states this claim. 2
  • Classified as probably not a substantial claim. 35
  • May combine two claims.

    Findingown data

    The other two Sncg met-types had few cells (n=3 and n=2) but had fairly distinctive properties.

    “The other two Sncg met-types had few cells (n=3 and n=2) but fairly distinctive properties.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    Nearly all t- and met-types in each subclass are arranged along cortical depth, with soma locations often centered in a layer or sublayer and continuous variation within and between types.

    “5) Unexpectedly, we found that nearly all t- and met-types in each subclass are arranged along the cortical depth; the soma locations of each type are often centered in a layer or sublayer, with continuous variations both within and between types.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    Vip-MET-1 typically showed regular, sustained firing, while Vip-MET-2 firing was usually irregular.

    “Vip-MET-1 also typically had regular, sustained firing while Vip-MET-2 firing was usually irregular (Figure 7L).”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    Vip-MET-3 was located in layer 5 and had short bitufted dendrites and complex axon elaboration at layer borders.

    “Vip-MET-3 was found in L5 (Figure 7I) and had short, bitfuted dendrites and complex axon elaboration at layer borders.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    These met-types were fairly cohesive in low-dimensional projections and could be identified by marker gene combinations.

    “These met-types were fairly cohesive in low-dimensional projections of transcriptomic and electrophysiological space (Figure 6B) and could be identified by particular combinations of marker genes”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    Some t-types were found at L1-L2/3 border, while others were distributed across L2/3.

    “some t-types were found right at the L1-L2/3 border (Vip Col15a1 Pde1a, Pvalb Vipr2), while others were distributed across L2/3 (Vip Chat Htr1f, Pvalb Tpbg)”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    Most t-types were strongly associated with a single met-type, and most met-types were composed of several t-types.

    “Most t-types were strongly associated with a single met-type, and most met-types were composed of several t-types”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    Pvalb-MET-4 was made up mainly of layer 4 and layer 2/3 fast-spiking cells, with some deeper cells, and had a layer 2/3-dominant axonal projection with sparse projections to deeper layers.

    “These consisted of mainly L4 and L2/3 fast-spiking cells (but included some deeper cells as well) with a L2/3-dominant axonal projection and sparse projections to deeper layers.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    Vip-MET-1 cells expressed Npy, whereas Vip-MET-2 cells expressed Ptprt and Rspo1.

    “Vip-MET-1 cells expressed Npy while Vip-MET-2 cells expressed Ptprt and Rspo1 (Figure 7K).”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    Most Lamp5 cells other than Lamp5 Lhx6 cells belonged to Lamp5-MET-1; the Lamp5 Lhx6 cells formed Lamp5-MET-2.

    “Most of the other Lamp5 cells were in the Lamp5-MET-1 type, except for the Lamp5 Lhx6 cells which formed Lamp5-MET-2.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    Lamp5-MET-2 could be distinguished by the presence or absence of several marker genes, was located in deep layers, and had electrophysiological properties similar to Lamp5-MET-1, including high upstroke-to-downstroke ratios and late-spiking.

    “Lamp5-MET-2 was distinguishable by the presence or absence of several marker genes (Figure 7B) and was found in deep layers; the electrophysiological properties resembled Lamp5-MET-1, with high-upstroke downstroke ratios and late-spiking.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    Vip-MET-1 cells were mainly in layers 2/3 and 4, had bitufted dendrites extending into layer 1, and had fairly concentrated axon innervation of lower layer 2/3.

    “Vip-MET-1 had cells primarily in L2/3 and L4, with bitufted dendrites extending into L1, and a fairly concentrated axon innervation of lower L2/3.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    Sncg-MET-3 cells were located deeply and belonged to the Sncg Slc17a8 transcriptomic type.

    “Sncg-MET-3 cells were deep and belonged to the Sncg Slc17a8 t-type.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    Some t-types had overlapping morpho-electric features, while others exhibited electrophysiological or morphological heterogeneity.

    “some t-types had overlapping morpho-electric features, while others exhibited electrophysiological (e.g., Sst Mme Fam114a1, Sst Tac1 Htr1d) or morphological (e.g., Sst Calb2 Pdlim5, Pvalb Reln Itm2a) heterogeneity.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    Action potential waveforms were similar among Pvalb met-types and had the fast-spiking shape.

    “AP shapes were quite consistent across the Pvalb met-types and were typical of a fast-spiking phenotype.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    Pvalb-MET-1 and Pvalb-MET-2 were located mainly in layers 5 and 6 and had basket-like morphology with axons and dendrites confined to the deep parts of those layers.

    “The first two met-types (Pvalb-MET-1 and Pvalb-MET-2) were found predominantly in L5 and L6 and had basket-like morphologies with axon and dendrites restricted to the deep part of L5 and L6.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    Sncg-MET-1 cells had bitufted or multipolar dendrites and a wide translaminar axon that mostly avoided layer 1.

    “These cells had bitufted or multipolar dendrites with wide, translaminar axon that mostly avoided L1.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    Deep Pvalb met-types could be separated by marker gene expression: Pvalb-MET-1 expressed Gabrg1, Bche, and Th, whereas Pvalb-MET-2 expressed Sema3e.

    “Marker genes also could distinguish these deep Pvalb met-types, as Pvalb-MET-1 cells expressed Gabrg1, Bche, and Th, while Pvalb-MET-2 cells expressed Sema3e (Figure 6G).”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    Morpho-electrical properties of GABAergic interneurons largely co-vary with transcriptomic types, and discrete and continuous variation coexist across the three modalities.

    “1) Morpho-electrical features of GABAergic interneurons largely co-vary with transcriptomic types, with discrete and continuous variations co-existing along the three modalities.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    Vip-MET-4 was located in lower layer 2/3 and innervated layers 2/3 through 6, similar to Vip-MET-2.

    “Vip-MET-4 was found in lower L2/3 and innervated L2/3 through L6 similar to Vip-MET-2.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    Axons of many types target specific layers, which is a hallmark distinction between met-types; differential axon targeting specificity redefines the traditional concept of Sst interneuron types.

    “6) The axons of many types also target specific layers, and this is a hallmark distinction between met-types; in particular, differential axon targeting specificity redefines the traditional concept of Sst interneuron types.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    At one end of the PC-3 spectrum, cells had low Npy expression, wide axons, and fewer late-spiking cells; at the other end, cells expressed more Npy, had rounder axons, and were consistently late-spiking.

    “One end of the spectrum defined by PC-3 had cells with low Npy expression, wide axons, and fewer cells with a late-spiking phenotype, while the other end had cells expressing more Npy with rounder axons that were consistently late-spiking.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    Sncg-MET-2 cells expressed Car10 and Nptx2, had very high input resistance, and were located at the layer 1-layer 2/3 border.

    “Sncg-MET-2 cells expressed Car10 and Nptx2 (Figure 7G), had very high input resistances (Figure 7H), and were found at the L1-L2/3 border (Figure 7E).”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingcitation

    Lamp5-MET-1 cells had action potentials with high upstroke-to-downstroke ratios and neurogliaform-like morphology, and were found mainly in layers 1 and 2/3 but also in deeper layers.

    “Lamp5-MET-1 had APs with high upstroke/downstroke ratios and a neurogliaform-like morphology (Jiang et al., 2013; Jiang et al., 2015; Schuman et al., 2019); these cells were found primarily in L1 and L2/3 but also appeared in deeper cortical layers.”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites Jiang et al., 2013 source

      Not checked in the free run.

    • cites Jiang et al., 2015 source

      Not checked in the free run.

    • cites Schuman et al., 2019 source

      Not checked in the free run.

  • May combine two claims.

    Findingown data

    Vip-MET-4 had enriched layer 4 axonal innervation, showed irregular and/or transient firing, and had more hyperpolarization-evoked sag than the first three Vip met-types.

    “However, these cells had enriched L4 axonal innervation; they also exhibited irregular and/or transient firing and had more hyperpolarization-evoked sag than the first three Vip met-types (Figure 7L).”
    Quote in the paperNot a substantial claim
  • The quote only partly states this claim.

    Findingown data

    Vip-MET-5 cells also frequently fired bursts near rheobase.

    “These cells also frequently fired bursts near rheobase.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    Pvalb-MET-3 cells mapped to Pvalb Reln Tac1 and were mostly layer 5 fast-spiking cells with dominant layer 5 axon innervation and a few collaterals extending superficially.

    “Pvalb-MET-3 had cells that mapped to Pvalb Reln Tac1 and contained mostly L5 fast-spiking cells with L5-dominant axon innervation and a few collaterals extending into superficial layers.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    Vip-MET-2 had a laminar position similar to Vip-MET-1 but longer dendrites, a narrower profile, and wider axonal branching only in deep layers.

    “Vip-MET-2 had a similar laminar position to Vip-MET-1 but with longer dendrites and a narrower profile with wider axonal branching only in deep layers.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    The study identifies 13 Sst met-types, substantially more than reported in previous morphological and/or electrophysiological studies.

    “We identify 13 Sst met-types (Figure 6), which is substantially more than described in previous morphological and/or electrophysiological studies (Kawaguchi and Kubota, 1996; McGarry et al., 2010; Markram et al., 2015; Jiang et al., 2015; Munõz et al., 2017).”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites Kawaguchi and Kubota, 1996 source

      Not checked in the free run.

    • cites McGarry et al., 2010

      Not checked in the free run.

    • cites Markram et al., 2015 source

      Not checked in the free run.

  • May combine two claims.

    Findingown data

    A major insight is that the somas of many GABAergic t- or met-types are restricted to a single cortical layer or sublayer, and Sst interneurons elaborate axons in a dominant cortical layer.

    “A major insight gained from our study is that the somas of many GABAergic t- or met-types are restricted to a single cortical layer or sublayer (Figure 2) and, in the case of Sst interneurons, elaborate their axons in a dominant cortical layer (Figure 4).”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    All Sst met-types contain at least one cell with some layer 1 projection and could technically be considered a Martinotti cell, usually the T-shaped type.

    “However, all these Sst met-types contain at least one cell that had some degree of L1 projection and could therefore technically be considered a Martinotti cell (usually the T-shaped) as well.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    Sst-MET-2 densely innervates layer 2/3 and largely avoids layer 1.

    “For example, Sst-MET-2 densely innervates L2/3 and largely avoids L1.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    Sst-MET-8 neurons, which map to Sst Hpse Cbln4 and are one of two major Sst met-types in layer 4, extensively innervate layer 4 and innervate layer 1 less.

    “The axons of Sst-MET-8 neurons (mapping to the Sst Hpse Cbln4 t-type) — one of two major Sst met-types found in L4 — extensively innervate L4 and innervate L1 to a lesser degree.”
    Quote in the paperSubstantial claim
  • Classified as probably not a substantial claim.

    Premisereasoning

    scRNAseq provides a promising new way to define cell types due to high dimensionality and scalability.

    “Recent advances in the collection and analysis of single cell RNA-sequencing (scRNAseq) data provide a promising new way to define cell types and how they relate to one another”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites Saunders et al., 2018 source

      Not checked in the free run.

    • cites Tasic et al., 2018 source

      Not checked in the free run.

    • cites Zeisel et al., 2018 source

      Not checked in the free run.

  • Classified as probably not a substantial claim. May combine two claims.

    Study design and conductown data

    The mapping method compared marker gene expression at each branch point and robustness was assessed by bootstrap.

    “The mapping method was based on comparing a cell’s marker genes expression at each branch point of the reference hierarchical transcriptomic tree with the marker genes expression of the reference cell types (Methods, Figure S1D); robustness was assessed by a bootstrap approach (Methods).”
    Quote in the paperSubstantial claim
  • Classified as probably not a substantial claim.

    Study design and conductnone given

    The mapping procedure was designed to minimize contamination from nearby non-neuronal cells and glutamatergic neurons.

    “Our mapping procedure for GABAergic neurons was designed to minimize the contribution of contamination from nearby non-neuronal cells (such as glia) and glutamatergic neurons.”
    Quote in the paperSubstantial claim
  • Classified as probably not a substantial claim.

    Premisecitation

    The field has not readily converged on a consensus number or definition of neuronal cell types.

    “the field has not readily converged on a consensus number, or even definition, of neuronal cell types”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites Ascoli et al., 2008 source

      Not checked in the free run.

    • cites DeFelipe et al., 2013 source

      Not checked in the free run.

    • cites Tebaykin et al., 2018 source

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Study design and conductreasoning

    Analyses by t-type were restricted to the 2,955 highly-consistent cells to limit mapping ambiguities.

    “When we performed analyses by t-type, we restricted the data set to the 2,955 cells with highly-consistent mapping to limit the effect of mapping ambiguities due to technical issues on our results”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Prior work has linked Sncg neurons by gene expression to Vip+/Cck+ basket cells.

    “Based on gene expression, Sncg neurons have been linked to Vip+/Cck + basket cells (Tasic et al., 2018).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Tasic et al., 2018 source

      Not checked in the free run.

  • Classified as probably not a substantial claim. May combine two claims.

    Premisecitation

    Scala et al. reported a continuum of morphological and electrophysiological variability in mouse primary motor cortex glutamatergic and GABAergic neurons, where similar transcriptomic types often have similar morpho-electric features without clear boundaries.

    “Consistent with our results, (Scala et al., 2020) describe a continuum of variability in the morphology and electrophysiology of glutamatergic and GABAergic neurons in primary motor cortex of the mouse — similar transcriptomic cell types frequently exhibit similar morpho-electric features, often without clear boundaries between them.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Scala et al., 2020

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Que et al. reported that neurons mapping to distinct Pvalb transcriptomic types in mouse hippocampus have qualitatively similar morphological characteristics.

    “Also, (Que et al., 2020) report that neurons mapping to distinct Pvalb t-types in the mouse hippocampus exhibit qualitatively similar morphological characteristics.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Que et al., 2020

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data

    The 28 met-types are labeled by salient gene markers and offer a systematic framework that encapsulates historical knowledge of cortical interneuron types.

    “4) The 28 met-types are labeled by salient gene markers and provide a systematic framework to encapsulate historical knowledge of cortical interneuron types.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Interpretationcitation

    Marker genes selective for particular t- or met-types have been mapped in mouse primary motor cortex by MERFISH, and they may have similar distributions in visual cortex because GABAergic t-types are shared across cortical areas.

    “The anatomical distribution of the marker genes selective for specific t- or met-types have been characterized in a recent MERFISH study in the mouse primary motor cortex (MOp) (Zhang et al., 2020); they may be similarly distributed in the visual cortex since GABAergic t-types are shared across cortical areas (Tasic et al., 2018).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Zhang et al., 2020

      Not checked in the free run.

    • cites Tasic et al., 2018 source

      Not checked in the free run.

  • May combine two claims.

    Interpretationcitation

    The two ends of the PC-3 spectrum resembled layer 1 interneuron populations from a recent barrel cortex study: cells with higher Npy expression matched Ndnf+/Npy+ neurogliaform cells, and the opposite end resembled canopy cells.

    “We noted that each end of the spectrum resembled populations of L1 interneurons described in a recent study in barrel cortex (Schuman et al., 2019): the cells here with higher Npy expression have electrophysiology and morphology consistent with Ndnf+/Npy+ neurogliaform cells, and those at the other end have properties more similar to the “canopy cells” described in that study.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Schuman et al., 2019 source

      Not checked in the free run.

  • May combine two claims.

    Interpretationreasoning

    The limited set of stimuli in the patch-clamp protocol, the relatively small number of morphological reconstructions, and the lower dimensionality of electrophysiological and morphological data may all contribute to the difference in granularity.

    “The limited number of stimuli in our standardized patch clamp protocol, the relatively small number of morphological reconstructions, and the much lower dimensionality of electrophysiological and morphological data compared to transcriptomic data may all contribute to this difference.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Recent evidence suggests that different morphological phenotypes correspond to different synaptic connectivity profiles.

    “Recent evidence also suggests that different morphological phenotypes correspond to differential synaptic connectivity profiles (Nigro et al., 2018; Naka et al., 2019; Scala et al., 2019).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Nigro et al., 2018 source

      Not checked in the free run.

    • cites Naka et al., 2019 source

      Not checked in the free run.

    • cites Scala et al., 2019 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    There is no absolute definition of a Martinotti cell based on the total amount of axon in layer 1, although it is generally described as significant.

    “We are not aware of an absolute definition of a Martinotti cell in terms of total amount of axon in L1, though it is generally described as “significant” (Tremblay et al., 2016; Zhou et al., 2020).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Tremblay et al., 2016 source

      Not checked in the free run.

    • cites Zhou et al., 2020 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    The authors made every effort to produce a fully connected neuronal structure while staying faithful to the image data.

    “Every attempt was made to generate a completely connected neuronal structure while remaining faithful to image data.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductreasoning

    No randomization was used during data collection because there was a single experimental condition for all acquired data.

    “No randomization was used during data collection as there was a single experimental condition for all acquired data.”
    Quote in the paperNot a substantial claim
  • Classified as probably not a substantial claim. May combine two claims.

    Study design and conductnone given

    A cell was labeled highly consistent if the sum of its two highest mapping probabilities exceeded 70% and the ratio of the top probability to the next was greater than 2; otherwise it was moderately consistent.

    “If the sum of the first two highest mapping probabilities for a cell was more than 70% and the ratio of the mapping probability of the first type to the next highest was more than 2, then the cell was labeled as “highly consistent.” Otherwise the cell was labeled “moderately consistent” (Figure S1G).”
    Quote in the paperSubstantial claim
  • Classified as probably not a substantial claim. May combine two claims.

    Study design and conductnone given

    Individual sweeps were included only if bridge balance was below 20 MΩ and below 15% of input resistance, bias current was within 0 ± 100 pA, and root mean square noise was below 0.07 mV in a short window and below 0.5 mV in a longer window.

    “For an individual sweep to be included, the following criteria were applied: (1) the bridge balance was <20 MΩ and <15% of the Rinput; (2) bias (leak) current 0 ± 100 pA; and (3) root mean square noise measurements in a short window (1.5 ms, to gauge high frequency noise) and longer window (500 ms, to measure patch instability) <0.07 mV and 0.5 mV, respectively.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing).

    Interpretationcitation

    This result suggests that transcriptomic types may need revision by combining another modality, such as connectivity, through supervised clustering to improve consistency.

    “This intriguing result suggests that transcriptomic types may be revised based on the combination with another modality (e.g., connectivity) via approaches such as supervised clustering to achieve better consistency.”
    Quote in the paperNot a substantial claim
  • Classified as probably not a substantial claim.

    Study design and conductown data

    Two principal components that correlated with collection method were removed from the UMAP visualization to reduce technical bias.

    “two PCs that exhibited high correlation with collection method (Pearson’s r = 0.94 and 0.22) were removed to reduce the effects of technical bias in the plots.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductreasoning

    The bath and internal solutions and preparation methods were chosen to maximize tissue quality, match common field solutions, reduce RNAse activity, and maximize mRNA recovery.

    “The composition of bath and internal solution as well as preparation methods were made to maximize the tissue quality of slices from adult mice, to align with solution compositions typically used in the field (to maximize the chance of comparison to previous studies), modified to reduce RNAse activity and ensure maximal gain of mRNA content.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    All procedures were carried out in accordance with the Institutional Animal Care and Use Committee at the Allen Institute for Brain Science.

    “all procedures were carried out in accordance with the Institutional Animal Care and Use Committee at the Allen Institute for Brain Science.”
    Quote in the paperNot a substantial claim
  • Classified as probably not a substantial claim. May combine two claims.

    Study design and conductown data

    Patch-seq transcriptomes were mapped top-down on the reference taxonomy tree by correlation with branch-point markers, with 100 bootstrap iterations sampling 70% of reference cells and 70% of markers to assess mapping robustness.

    “The Patch-seq transcriptomes were mapped to the reference taxonomy tree in the top down manner, trying to resolve broad classes first, followed by subclasses and types (Figure S1C and D). For each single cell transcriptome, starting from the root and at each branch point, we computed its correlation with the reference cell types using the markers associated with the given branch point (i.e., the”
    Quote in the paperSubstantial claim
  • Classified as probably not a substantial claim. May combine two claims.

    Study design and conductnone given

    For inclusion in analysis, a cell had to have a seal greater than 1 GΩ before break-in and an initial access resistance below 20 MΩ and below 15% of input resistance.

    “To be included in the analysis, a cell needed to have a >1 GΩ seal recorded before break-in and an initial access resistance <20 MΩ and <15% of the Rinput.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Brains were sliced either coronally or at a 17° angle from the coronal plane to preserve the intactness of neuronal processes in visual cortex.

    “Brains were mounted for slicing either in the coronal plane or at a 17° angle from the coronal plane to preserve the intactness of neuronal processes in the visual cortex.”
    Quote in the paperNot a substantial claim
  • Classified as probably not a substantial claim. May combine two claims.

    Premisenone given

    Multiple populations can be distinct yet still overlap substantially, which makes it hard to determine the origin of a given cell.

    “Even if multiple populations are different, they may heavily overlap, making it difficult to tell where a given cell came from; we used supervised classifiers to estimate how reliable predictions about type could be using different modalities.”
    Quote in the paperSubstantial claim
  • Classified as probably not a substantial claim. May combine two claims.

    Premisereasoning

    A two-component model would yield a higher likelihood from overfitting even when the underlying distributions are identical, so the significance of the observed LLR was evaluated using parametric bootstrap.

    “Since the two-component model would produce a higher likelihood due to overfitting even if the underlying distributions were the same, the statistical significance of the observed LLR was assessed by parametric boostrap.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductreasoning

    The study did not blind data collection or analysis to the experimental conditions, as there was only one condition for all data.

    “Data collection and analyses were not performed blind to the conditions of the experiments as there was a single experimental condition for all acquired data.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    The various stimulus protocols were not given in a randomized sequence.

    “The different stimulus protocols were not presented in a randomized order.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    NBLAST compares two morphologies by examining the distance and local direction of nearby points between them.

    “This method compares a pair of morphologies by analyzing the distance and local direction of nearby points between the two structures.”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Costa et al., 2016 source

      Not checked in the free run.

    • cites Kohl et al., 2013 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Kim et al. found that long-range connections from visual cortex layer 2/3 neurons correlate not with transcriptomic types but with gene expression differences within types.

    “A recent study showed that long-range connections from visual cortex layer 2/3 neurons do not correlate with transcriptomic types but rather with within-type gene expression differences (Kim et al., 2020).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Kim et al., 2020 source

      Not checked in the free run.

  • Classified as probably not a substantial claim. May combine two claims. The quote only partly states this claim.

    Study design and conductown data

    A feedforward neural network classifier was trained on reference cells split into 80% training and 20% test sets, and the training and prediction were repeated 100 times with new random training sets.

    “We built a feedforward neural network classifier which receives gene expression data as input to predict the cell type for each individual cell. To train the classifier, we used the reference cells and their corresponding types. The reference cells were divided into two groups of training (80%) and test (20%) sets.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductnone given

    The study did not use statistical methods to predetermine sample sizes, but its sample sizes are similar to those in previous publications.

    “No statistical methods were used to predetermine sample sizes, but the sample sizes here are similar to those reported in previous publications.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Interpretationown data

    These met-types represent a unified definition of cortical GABAergic interneuron types based on multimodal experimental data and enable cross-modal feature prediction.

    “These met-types represent a version of a unified definition of cortical GABAergic interneuron types established with multimodal experimental data and enabling cross-modal feature prediction.”
    Quote in the paperSubstantial claim
  • Classified as probably not a substantial claim.

    Study design and conductnone given

    Cells with inconsistent mapping were excluded from analyses that used transcriptomic type assignments.

    “Cells with “inconsistent” mapping were not used in analyses that incorporated t-type assignments.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductreasoning

    Features that were mainly determined by z-dimension differences were excluded from analysis to reduce technical artifacts from z-compression after slice processing.

    “While slice angle tilt and shrinkage correction were performed (see above), features predominantly determined by differences in the z-dimension were not analyzed to minimize technical artifacts due to z-compression of the slice after processing.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Multiplex FISH is already used to measure the proportions of transcriptomic types in brain tissue.

    “In addition, multiplex FISH is already being used to measure the proportions of transcriptomic types within a given brain tissue (Hodge et al., 2019; Moffitt et al., 2018; Zhang et al., 2020).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Hodge et al., 2019 source

      Not checked in the free run.

    • cites Moffitt et al., 2018 source

      Not checked in the free run.

    • cites Zhang et al., 2020

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data

    The results show that Sst neurons have clear laminar innervation preferences that vary across met-types, so dominant laminar targets may be a more reliable distinguishing feature than whether axon is present in layer 1.

    “These results reveal that Sst neurons have clear laminar innervation preferences that vary across met-types; consequently, their dominant laminar targets may be a more reliable distinguishing feature than the presence or absence of axon in layer 1.”
    Quote in the paperSubstantial claim
  • Classified as probably not a substantial claim.

    Study design and conductcitation

    Electrophysiological features were measured from short and long current pulses using methods previously described by Gouwens et al.

    “Electrophysiological features were measured from responses elicited by short (3 ms) current pulses and long (1 s) current steps as previously described (Gouwens et al., 2019).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Gouwens et al., 2019 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductreasoning

    Ndnf-IRES2-dgCre mice were not given trimethoprim because baseline dgCre activity was sufficient to label cells with the Ai14 reporter.

    “Ndnf-IRES2-dgCre animals did not receive trimethoprim induction, since the baseline dgCre activity (without trimethoprim) was sufficient to label the cells with the Ai14 reporter.”
    Quote in the paperNot a substantial claim
73 of 73
  • The paper relies on this without support.

    GABAergic interneuron morphology is better preserved in ~350 um thick in vitro slice preparations than glutamatergic pyramidal neuron morphology.

    “the morphology of GABAergic interneurons is better preserved in ~350 um thick in vitro slice preparations than that of glutamatergic pyramidal neurons with known long-range projections”
  • The paper relies on this without support.

    The morpho-electric profiles of most t-types are largely unknown and their correspondence to historically defined GABAergic types has not been established.

    “The morpho-electric profiles of most t-types, however, are largely unknown and their correspondence to historically defined GABAergic types has not been established.”
  • The paper relies on this without support.

    The mapping algorithms and quality thresholds reliably assign Patch-seq transcriptomes to the correct reference transcriptomic types.

    “For the reasons explained above, we used transcriptomes of dissociated cells from (Tasic et al., 2018) as reference dataset and mapped Patch-seq transcriptomes to the reference data to identify their cell types.”
  • The paper relies on this without support.

    The standardized patch-clamp protocol and morphological reconstructions capture the relevant electrophysiological and morphological properties that distinguish cell types.

    “The limited number of stimuli in our standardized patch clamp protocol, the relatively small number of morphological reconstructions, and the much lower dimensionality of electrophysiological and morphological data compared to transcriptomic data may all contribute to this difference.”
  • The paper relies on this without support.

    The marker genes used to label met-types are selective for those met-types.

    “Marker genes also could distinguish these deep Pvalb met-types, as Pvalb-MET-1 cells expressed Gabrg1, Bche, and Th, while Pvalb-MET-2 cells expressed Sema3e (Figure 6G).”
5 of 5

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Transcriptomically defined cell types have been shown to exhibit concordant morphological and physiological properties.

    “Transcriptomically defined cell types have been shown to exhibit concordant morphological and physiological properties10,11.”
  • A parallel Patch-seq study of the inhibitory neurons in the mouse visual cortex focused on isolating multimodal neural types but also often observed continuous variation.

    “A parallel Patch-seq study of the inhibitory neurons in the mouse visual cortex45 focused on isolating multimodal neural types (‘met-types’) but also often observed continuous variation.”
  • These visual cortex GABAergic MET types show strong cross-modality concordance and mutual predictability.

    “These visual cortex GABAergic MET types show robust cross-modality concordance and mutual predictability.”

    From What is a cell type and how to define it? (2022) · cites this paper as Gouwens et al., 2020

  • To reduce heterogeneity at the individual type level, triple-modality MET types were defined at a granularity between transcriptomic subclasses and types.

    “To overcome heterogeneity at individual type level, a set of triple-modality MET types are defined at an intermediate level of granularity (between transcriptomic subclasses and types).”

    From What is a cell type and how to define it? (2022) · cites this paper as Gouwens et al., 2020

  • A Patch-seq study of mouse visual cortical GABAergic neurons found relatively high corresponding continuous variation of transcriptomic types with cortical-depth anatomical distribution and morpho-electrical properties.

    “Another Patch-seq study of mouse visual cortical GABAergic neurons also reveals a relatively high degree of corresponding continuous variations of transcriptomic types with their anatomical distribution along the cortical depth and the variations of their morpho-electrical properties (Fig. 3B) (Gouwens et al., 2020).”

    From What is a cell type and how to define it? (2022) · cites this paper as Gouwens et al., 2020

Cites

Flagged first, then by citations

7 of the 99 references couldn’t be matched to a known paper.

Cited by

Sorted by citations

Authors
Gouwens, N. W., Sorensen, S. A., Baftizadeh, F., Budzillo, A., Lee, B. R., Jarsky, T., Alfiler, L., Baker, K., Barkan, E., Berry, K., Bertagnolli, D., Bickley, K., Bomben, J., Braun, T., Brouner, K., Casper, T., Crichton, K., Daigle, T. L., Dalley, R., de Frates, R. A., Dee, N., Desta, T., Lee, S. D., Dotson, N., Egdorf, T., Ellingwood, L., Enstrom, R., Esposito, L., Farrell, C., Feng, D., Fong, O., Gala, R., Gamlin, C., Gary, A., Glandon, A., Goldy, J., Gorham, M., Graybuck, L., Gu, H., Hadley, K., Hawrylycz, M. J., Henry, A. M., Hill, D., Hupp, M., Kebede, S., Kim, T. K., Kim, L., Kroll, M., Lee, C., Link, K. E., Mallory, M., Mann, R., Maxwell, M., McGraw, M., McMillen, D., Mukora, A., Ng, L., Ng, L., Ngo, K., Nicovich, P. R., Oldre, A., Park, D., Peng, H., Penn, O., Pham, T., Pom, A., Popović, Z., Potekhina, L., Rajanbabu, R., Ransford, S., Reid, D., Rimorin, C., Robertson, M., Ronellenfitch, K., Ruiz, A., Sandman, D., Smith, K., Sulc, J., Sunkin, S. M., Szafer, A., Tieu, M., Torkelson, A., Trinh, J., Tung, H., Wakeman, W., Ward, K., Williams, G., Zhou, Z., Ting, J. T., Arkhipov, A., Sümbül, U., Lein, E. S., Koch, C., Yao, Z., Tasic, B., Berg, J., Murphy, G. J., & Zeng, H.
Affiliations
  • Allen Institute for Brain Science (US)
  • University of Washington (US)
Corresponding author
  • Gouwens, Nathan W.
  • Sorensen, Staci A.
  • Murphy, Gabe J.
Venue
Cell
Publisher
Elsevier BV
Published
2020-11
Volume
183
Issue
4
Pages
935-953.e19
ISSN
0092-8674 (ISSN-L)
OpenAlex
W3101846945
Cited by
538
References
99
Citations by year
2026: 59 · 2025: 98 · 2024: 105 · 2023: 109 · 2022: 80 · 2021: 68 · 2020: 18
FWCI
31.49
Type
journal article
Language
en
Open access
Locations
  • Cell (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
Funders
National Institutes of Health
Topics
  • Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Neuroscience and Neuropharmacology Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
  • Life Sciences › Neuroscience › Cognitive Neuroscience › Neural dynamics and brain function
Keywords
GABAergic interneurons, visual cortex, neuronal cell types, neuronal morphology, electrophysiological properties, multimodal integration, mice
MeSH terms
Animals, Cerebral Cortex, Female, Hippocampus, Ion Channels, Male, Mice, Inbred C57BL, Nerve Tissue Proteins, Gene Expression Profiling, Electrophysiological Phenomena, GABAergic Neurons, Transcriptome

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-07.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-07.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review