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Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells
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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.
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“for most types, the cells mapping to a t-type exhibit consistent electrophysiological and morphological properties”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Abstract
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“We find that most transcriptomic types (t-types) occupy specific laminar positions within visual cortex”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Abstract
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“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.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Relating neurons assayed via Patch-seq recordings to transcriptomic types
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- Not checked yetcites Tripathy et al., 2018 source
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“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”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Relating neurons assayed via Patch-seq recordings to transcriptomic types
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In the paper
“the two transcriptomic datasets had similar structure when visualized together via a Uniform Manifold Approximation and Projection (UMAP, (Becht et al., 2018)) method”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Relating neurons assayed via Patch-seq recordings to transcriptomic types
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In the paper
“We identify layer-specific axon innervation pattern as a defining feature distinguishing different met-types.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Abstract
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“We found that 3,855 of the 4,270 cells had consistent t-type mapping (2,955 “highly consistent” and 900 “moderately consistent””
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Relating neurons assayed via Patch-seq recordings to transcriptomic types
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In the paper
“These properties display both discrete and continuous variation among t-types.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Abstract
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In the paper
“Through multimodal integrated analysis we define 28 met-types that have congruent morphological, electrophysiological, and transcriptomic properties and robust mutual predictability.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Abstract
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“compared to those of equivalent dissociated cells, the transcriptomes of cells obtained by Patch-seq recordings more frequently exhibit “dropout””
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Relating neurons assayed via Patch-seq recordings to transcriptomic types
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“The other two Sncg met-types had few cells (n=3 and n=2) but fairly distinctive properties.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Characteristics of met-types
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“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.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Discussion
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In the paper
“Vip-MET-1 also typically had regular, sustained firing while Vip-MET-2 firing was usually irregular (Figure 7L).”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Characteristics of met-types
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“Vip-MET-3 was found in L5 (Figure 7I) and had short, bitfuted dendrites and complex axon elaboration at layer borders.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Characteristics of met-types
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“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”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Characteristics of met-types
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“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)”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Relating neurons assayed via Patch-seq recordings to transcriptomic types
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In the paper
“Most t-types were strongly associated with a single met-type, and most met-types were composed of several t-types”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Integrated classification of GABAergic neurons by correspondence between transcriptomic and morpho-electric types
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“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.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Characteristics of met-types
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“Vip-MET-1 cells expressed Npy while Vip-MET-2 cells expressed Ptprt and Rspo1 (Figure 7K).”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Characteristics of met-types
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“Most of the other Lamp5 cells were in the Lamp5-MET-1 type, except for the Lamp5 Lhx6 cells which formed Lamp5-MET-2.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Characteristics of met-types
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“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.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Characteristics of met-types
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In the paper
“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.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Characteristics of met-types
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In the paper
“Sncg-MET-3 cells were deep and belonged to the Sncg Slc17a8 t-type.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Characteristics of met-types
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In the paper
“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.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Integrated classification of GABAergic neurons by correspondence between transcriptomic and morpho-electric types
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In the paper
“AP shapes were quite consistent across the Pvalb met-types and were typical of a fast-spiking phenotype.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Characteristics of met-types
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In the paper
“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.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Characteristics of met-types
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“These cells had bitufted or multipolar dendrites with wide, translaminar axon that mostly avoided L1.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Characteristics of met-types
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In the paper
“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).”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Characteristics of met-types
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In the paper
“1) Morpho-electrical features of GABAergic interneurons largely co-vary with transcriptomic types, with discrete and continuous variations co-existing along the three modalities.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Discussion
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“Vip-MET-4 was found in lower L2/3 and innervated L2/3 through L6 similar to Vip-MET-2.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Characteristics of met-types
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In the paper
“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.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Discussion
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In the paper
“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.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Characteristics of met-types
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In the paper
“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).”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Characteristics of met-types
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In the paper
“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.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Characteristics of met-types
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In the paper
“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).”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Characteristics of met-types
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In the paper
“These cells also frequently fired bursts near rheobase.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Characteristics of met-types
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In the paper
“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.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Characteristics of met-types
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In the paper
“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.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Characteristics of met-types
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In the paper
“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).”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Discussion
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“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).”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Discussion
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In the paper
“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.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Discussion
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In the paper
“For example, Sst-MET-2 densely innervates L2/3 and largely avoids L1.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Discussion
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In the paper
“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.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Discussion
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In the paper
“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”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Introduction
What the sources say
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In the paper
“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).”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Relating neurons assayed via Patch-seq recordings to transcriptomic types
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In the paper
“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.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Relating neurons assayed via Patch-seq recordings to transcriptomic types
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In the paper
“the field has not readily converged on a consensus number, or even definition, of neuronal cell types”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Introduction
What the sources say
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In the paper
“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”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Relating neurons assayed via Patch-seq recordings to transcriptomic types
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In the paper
“Based on gene expression, Sncg neurons have been linked to Vip+/Cck + basket cells (Tasic et al., 2018).”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Characteristics of met-types
What the sources say
- Not checked yetcites Tasic et al., 2018 source
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In the paper
“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.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Discussion
What the sources say
- Not checked yetcites Scala et al., 2020
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In the paper
“Also, (Que et al., 2020) report that neurons mapping to distinct Pvalb t-types in the mouse hippocampus exhibit qualitatively similar morphological characteristics.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Discussion
What the sources say
- Not checked yetcites Que et al., 2020
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In the paper
“4) The 28 met-types are labeled by salient gene markers and provide a systematic framework to encapsulate historical knowledge of cortical interneuron types.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Discussion
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“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).”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Characteristics of met-types
What the sources say
- Not checked yetcites Zhang et al., 2020
- Not checked yetcites Tasic et al., 2018 source
Strength:hedged· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
In the paper
“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.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Results > Characteristics of met-types
What the sources say
- Not checked yetcites Schuman et al., 2019 source
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Discussion
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“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).”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Discussion
What the sources say
Strength:hedged· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“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).”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Discussion
What the sources say
Strength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Every attempt was made to generate a completely connected neuronal structure while remaining faithful to image data.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > STAR Methods > METHOD DETAILS
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“No randomization was used during data collection as there was a single experimental condition for all acquired data.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > STAR Methods > METHOD DETAILS
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“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).”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > STAR Methods > METHOD DETAILS
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > STAR Methods > METHOD DETAILS
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Discussion
Strength:hedged· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✗ Checkable: fails✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. It may be too vague to check against evidence. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > STAR Methods > METHOD DETAILS
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > STAR Methods > METHOD DETAILS
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“all procedures were carried out in accordance with the Institutional Animal Care and Use Committee at the Allen Institute for Brain Science.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > STAR Methods > EXPERIMENTAL MODEL AND SUBJECT DETAILS
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“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”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > STAR Methods > METHOD DETAILS
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > STAR Methods > METHOD DETAILS
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > STAR Methods > METHOD DETAILS
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > STAR Methods > METHOD DETAILS
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > STAR Methods > METHOD DETAILS
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > STAR Methods > METHOD DETAILS
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“The different stimulus protocols were not presented in a randomized order.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > STAR Methods > METHOD DETAILS
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“This method compares a pair of morphologies by analyzing the distance and local direction of nearby points between the two structures.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > STAR Methods > METHOD DETAILS
What the sources say
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“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).”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Discussion
What the sources say
- Not checked yetcites Kim et al., 2020 source
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > STAR Methods > METHOD DETAILS
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim. It may state two separate claims as one. The quote only partly states this claim.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“No statistical methods were used to predetermine sample sizes, but the sample sizes here are similar to those reported in previous publications.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > STAR Methods > METHOD DETAILS
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Discussion
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Cells with “inconsistent” mapping were not used in analyses that incorporated t-type assignments.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > STAR Methods > METHOD DETAILS
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > STAR Methods > METHOD DETAILS
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“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).”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Discussion
What the sources say
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > Discussion
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
In the paper
“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).”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > STAR Methods > METHOD DETAILS
What the sources say
- Not checked yetcites Gouwens et al., 2019 source
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells > STAR Methods > EXPERIMENTAL MODEL AND SUBJECT DETAILS
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
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).”
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?
The cited source says what the claim attributes to it.
In the citing paper
“Transcriptomically defined cell types have been shown to exhibit concordant morphological and physiological properties10,11.”
From A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain (2023) · cites this paper as [10]
In the citing paper
“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.”
From Phenotypic variation of transcriptomic cell types in mouse motor cortex (2021) · cites this paper as [45]
In the citing paper
“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
In the citing paper
“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
In the citing paper
“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
In the citing paper
“using the Patch-seq approach, we simultaneously profiled the transcriptomic, electrophysiological, and morphological properties of a large set of GABAergic interneurons from mouse visual cortex and found excellent correspondence among the three modalities”
From A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation (2021) · cites this paper as Gouwens et al., 2020
In the citing paper
“These studies demonstrate the validity and power of using the highly scalable scRNA-seq approach to generate a comprehensive census of cell types as a foundation for further structural and functional studies of brain circuits.”
From A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation (2021) · cites this paper as Gouwens et al., 2020
In the citing paper
“Since isocortical Sst Myh8 and Etv1 cells are L5 Martinotti cells (Gouwens et al., 2020) (Fig. S1B), the HPF Myh8 and Etv1 cells are likely the Martinotti-like oriens lacunosum-moleculare (OLM) cells (Leao et al., 2012).”
From A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation (2021) · cites this paper as Gouwens et al., 2020
Citations
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STAR: ultrafast universal RNA-seq aligner
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Dimensionality reduction for visualizing single-cell data using UMAP
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Software for Computing and Annotating Genomic Ranges
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Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq
Zeisel, A., Muñoz-Manchado, A. B., Codeluppi, S., Lönnerberg, P., La Manno, G., Juréus, A., Marques, S., Munguba, H., He, L., Betsholtz, C., et al. (2015) · Science · doi:10.1126/science.aaa1934 · Cited by 3,124 · cited 2×
“…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 (Saunders et al., 2018; Tasic et al., 2018; Zeisel et al., 2018; Zeisel et al., 2015; Tasic et al., 2016; Shekhar et al., 2016).”
BackgroundSpatially resolved, highly multiplexed RNA profiling in single cells
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BackgroundMolecular Architecture of the Mouse Nervous System
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Metadata
- 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.
- ORCID
- Gouwens, Nathan W.
- Sorensen, Staci A.
- Baftizadeh, Fahimeh
- Budzillo, Agata
- Lee, Brian R.
- Jarsky, Tim
- Alfiler, Lauren
- Baker, Katherine
- Barkan, Eliza
- Berry, Kyla
- Bertagnolli, Darren
- Bickley, Kris
- Bomben, Jasmine
- Braun, Thomas
- Brouner, Krissy
- Casper, Tamara
- Crichton, Kirsten
- Daigle, Tanya L.
- Dalley, Rachel
- Dee, Nick
- Desta, Tsega
- Lee, Samuel Dingman
- Dotson, Nadezhda
- Egdorf, Tom
- Ellingwood, Lauren
- Enstrom, Rachel
- Esposito, Luke
- Farrell, Colin
- Feng, David
- Fong, Olivia
- Gala, Rohan
- Gamlin, Clare
- Gary, Amanda
- Glandon, Alexandra
- Goldy, Jeff
- Gorham, Melissa
- Graybuck, Lucas
- Hadley, Kristen
- Hawrylycz, Michael J.
- Henry, Alex M.
- Hill, DiJon
- Hupp, Madie
- Kebede, Sara
- Kim, Tae Kyung
- Kim, Lisa
- Kroll, Matthew
- Lee, Changkyu
- Link, Katherine E.
- Mallory, Matthew
- Mann, Rusty
- Maxwell, Michelle
- McMillen, Delissa
- Mukora, Alice
- Ng, Lindsay
- Ng, Lydia
- Nicovich, Philip R.
- Oldre, Aaron
- Popović, Zoran
- Potekhina, Lydia
- Rajanbabu, Ramkumar
- Ransford, Shea
- Reid, David
- Rimorin, Christine
- Ronellenfitch, Kara
- Ruiz, Augustin
- Smith, Kimberly
- Sunkin, Susan M.
- Szafer, Aaron
- Tieu, Michael
- Torkelson, Amy
- Trinh, Jessica
- Tung, Herman
- Wakeman, Wayne
- Ward, Katelyn
- Williams, Grace
- Zhou, Zhi
- Ting, Jonathan T.
- Arkhipov, Anton
- Sümbül, Uygar
- Lein, Ed S.
- Yao, Zizhen
- Tasic, Bosiljka
- Berg, Jim
- Murphy, Gabe J.
- Zeng, Hongkui
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2020-11
- Volume
- 183
- Issue
- 4
- Pages
- 935-953.e19
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC7781065
- OpenAlex
- W3101846945
- Semantic Scholar
- 82788e871368c8e83c596996c4db302dd3f44074
- 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
- bronze
- doi.org
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (vor, 376 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- 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.
A language model drew the claims from the paper on 2026-10-07, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-10-07 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).
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.
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