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Cited by 2,995Single-cell and spatial transcriptomicsNeurogenesis and neuroplasticity mechanismsNeuroscience and Neuropharmacology Research

Molecular Architecture of the Mouse Nervous System

Open access
Zeisel, Amit, Hochgerner, Hannah, Lönnerberg, Peter, Johnsson, Anna, Memic, Fatima, van der Zwan, Job, Häring, Martin, Braun, Emelie +12 more·2018·Cell
DOI 10.1016/j.cell.2018.06.021PMC PMC6086934

Published version of a preprint

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Abstract

The mammalian nervous system executes complex behaviors controlled by specialized, precisely positioned, and interacting cell types. Here, we used RNA sequencing of half a million single cells to create a detailed census of cell types in the mouse nervous system. We mapped cell types spatially and derived a hierarchical, data-driven taxonomy. Neurons were the most diverse and were grouped by developmental anatomical units and by the expression of neurotransmitters and neuropeptides. Neuronal diversity was driven by genes encoding cell identity, synaptic connectivity, neurotransmission, and membrane conductance. We discovered seven distinct, regionally restricted astrocyte types that obeyed developmental boundaries and correlated with the spatial distribution of key glutamate and glycine neurotransmitters. In contrast, oligodendrocytes showed a loss of regional identity followed by a secondary diversification. The resource presented here lays a solid foundation for understanding the molecular architecture of the mammalian nervous system and enables genetic manipulation of specific cell types.

AI snapshot

Written from the paper’s full text.

TL;DR

The paper uses single-cell RNA sequencing of ~half a million cells across 19 regions of the mouse nervous system to create a molecular census and data-driven taxonomy of cell types. It reports that nervous system organization reflects major cell class, developmental origin, and neurotransmitter type, with regionally specified astrocytes and a loss of regional patterning in the oligodendrocyte lineage.

Key findings

  • The survey analyzed 509,876 cells and retained a final curated compendium of 265 clusters represented by 160,796 high-quality single-cell transcriptomes; 248 (93%) clusters were uniquely identifiable with just two genes, 17 required three genes, and none required more than three. A random forest classifier on held-out data achieved average precision and recall of 82%, and 98% of 139 previously published clusters were perfect or near-perfect matches.
  • Neurons were the most diverse class: PNS neurons segregated into sensory, sympathetic, and enteric subdivisions, while CNS neurons generally split first by anteroposterior domain and then by excitatory versus inhibitory neurotransmitter. The paper identified seven molecularly distinct astrocyte types with regionally restricted distributions, including telencephalon-specific ACTE1/ACTE2 and non-telencephalon ACNT1/ACNT2 separated by a sharp Mfge8/Agt border.
  • Oligodendrocyte lineage stages OPC, COP, and NFOL presented as single brain-wide common cell types regardless of tissue, indicating that mature oligodendrocyte diversity arises by secondary diversification rather than developmental patterning. Spinal cord and hindbrain oligodendrocytes retained Hox gene expression, but forebrain and midbrain patterning transcription factors were detected only at very low levels (<1% of cells) if at all.

Methods

  • Dissected 19 regions from adolescent mice (postnatal ages P12–30, plus 6- and 8-week-old mice), including brain, spinal cord, dorsal root ganglia, sympathetic ganglion, and enteric nervous system; used 133 samples and 10X Genomics Chromium droplet microfluidics, with FACS for enteric neural-crest-derived cells and some inhibitory neurons.
  • Developed and applied “cytograph,” a multistage pipeline including quality filtering, major-class SVM classification, multiscale KNN manifold learning, graph t-SNE, Polished Louvain clustering, gene enrichment, Bayesian trinarization, marker gene set discovery, and dendrogram construction.
  • Validated clusters by random forest classification, comparison with six published scRNA-seq datasets, RNAscope in situ hybridization, and spatial correlation of cluster expression profiles with Allen Mouse Brain Atlas ISH voxel data.

Limitations

  • Stated limitations: technical/experimental issues including doublets, sex-specific gene expression, and low-quality cells; sampling only a little more than half a million cells with relatively shallow sequencing likely misses additional structure and subtypes; differential survival or size selection biases may have lost cell types (e.g., Purkinje cells likely undersampled); clustering was conservative and did not analyze substantial remaining heterogeneity within clusters; and the work describes only molecular cell types without linking them to functional, anatomical, morphological, or electrophysiological properties.
  • Evident from the text: the survey omitted at least the retina, olfactory epithelium, vomeronasal organ, inner ear, and parasympathetic ganglia; enteric analysis covered only the myenteric plexus of the small intestine; and the authors note that interneurons were undersampled by scRNA-seq while astrocytes were undersampled by osmFISH.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1016/j.cell.2018.06.021

Cites

53 of 53 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

23 of 45 cited sources checked · 12 supported · 0 flagged · accuracy not yet measured

  • Study design and conductown data

    Concordance with six previously published scRNA-seq datasets showed that 98% of 139 previously published clusters were perfect or near-perfect matches to corresponding clusters in the new compendium.

    “Of the 139 previously published clusters, 98% were perfect or near-perfect matches to corresponding clusters in the new compendium (84% perfect, 14% near perfect, 2% mismatches; see Table S2).”
    Quote in the paperSubstantial claim1 of 3 sources checked
    • cites Zeisel et al., 2015 source
    • cites Muñoz-Manchado et al., 2018 source

      The Results section, “scRNA-Seq of Interneurons of the Dorsolateral Striatum” (page unavailable), reports nine clusters in Dataset B and 97% precision and 96% recall for a classifier, not matches to previously published clusters. Searches for “139,” “near-perfect matches,” and comparisons with six published datasets found no passage reporting the claimed 98% concordance or its breakdown. (LLM, conf=0.77)

      Experimental — accuracy not yet measured
    • cites Hochgerner et al., 2018 source
  • Findingown data

    Two VLMC types were distinguished by expression of genes including Il33 (VLMC1) and Ptgds (VLMC2).

    “Two types were distinguished by expression of genes including the pro-inflammatory cytokine Il33 (VLMC1) and the Prostaglandin D2 synthetase Ptgds (VLMC2), the latter previously found as the most highly enriched gene in mouse leptomeninges (Yasuda et al., 2013) (Figure S3A).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Yasuda et al., 2013 source

      The Microarray Analysis section identifies prostaglandin D2 synthase as an arachnoid-barrier marker in mouse leptomeninges, and the Establishment of Immortalized Mouse AB Cell Lines section reports strong staining for the protein. The citation is attached to the claim that Ptgds was the most highly enriched gene in mouse leptomeninges; our copy supports its expression there, but does not establish that ranking. The VLMC1/VLMC2 distinction is not the part attributed to Yasuda et al. by this citation. (LLM, conf=0.84)

      Experimental — accuracy not yet measured
  • Interpretationcitation

    Brain fibroblast-like cells are likely identical to the vascular leptomeningeal cells (VLMCs) previously described in the mouse CNS.

    “Brain fibroblast-like cells are likely identical to the vascular leptomeningeal cells (VLMCs) that we previously described in the mouse CNS (Marques et al., 2016).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Marques et al., 2016 source
  • Findingcitation

    We identified central canal neurons (SCINH11), known as cerebrospinal fluid-contacting neurons, which expressed Gata2 and Gata3.

    “In addition, here we identified central canal neurons (SCINH11), known as cerebrospinal fluid-contacting neurons, which expressed transcription factors Gata2 and Gata3 (Figure S7) (Petracca et al., 2016).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Petracca et al., 2016 source
  • Interpretationcitation

    OPCs have a common evolutionary origin with Schwann cells.

    “These observations, and the finding that OPCs align molecularly with all the neural-crest-derived glia, suggest that they are a neural-crest-like type of glia and support the view that they have a common evolutionary origin with Schwann cells (Kastriti and Adameyko, 2017).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Kastriti and Adameyko, 2017 source
  • Classified as probably not a substantial claim. 27
  • May combine two claims. 96
  • The quote only partly states this claim. 1

  • Classified as probably not a substantial claim.

    Premisecitation

    Single-cell RNA sequencing has emerged as a powerful method for unbiased discovery of cell types and states based on gene activity.

    “single-cell RNA sequencing (scRNA-seq) has emerged as a powerful method for unbiased discovery of cell types and states based on gene activity (Islam et al., 2011, Jaitin et al., 2014, Macosko et al., 2015, Ramsköld et al., 2012, Shekhar et al., 2016, Tang et al., 2009, Tasic et al., 2016, Usoskin et al., 2015, Zeisel et al., 2015)”
    Quote in the paperSubstantial claim3 of 3 sources checked
    • cites Islam et al., 2011 source

      The Discussion reports that single-cell expression profiling forms cell-type clusters without known markers or prior knowledge that a type exists, supporting unbiased discovery of cell types. It is more cautious about cell states: distinct substates may or may not be distinguishable by transcriptome analysis, so the claim overstates that part. (LLM, conf=0.88)

      Experimental — accuracy not yet measured
    • cites Jaitin et al., 2014 source
    • cites Macosko et al., 2015 source

  • May combine two claims.

    Premisecitation

    Oligodendrocyte morphology varies according to the type of axon they myelinate, but transplantation experiments indicate that those differences are plastic.

    “Oligodendrocyte morphology varies according to the type of axon they myelinate, but transplantation experiments indicate that those differences are plastic (Richardson et al., 2006).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Richardson et al., 2006 source

      The References (page unavailable) cite work on morphological heterogeneity of oligodendrocytes and on their not being inherently programmed to myelinate a specific axon size. However, the passages retrieved from our copy do not establish that morphology varies by the type of axon myelinated or that transplantation experiments demonstrate plasticity of those differences. (LLM, conf=0.73)

      Experimental — accuracy not yet measured

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

    Premisecitation

    Similar phenomena were recently reported in embryonic stem cells in vitro and, less dramatically, in the developing Drosophila brain.

    “Similar phenomena were recently reported in embryonic stem cells in vitro (Briggs et al., 2017) and, less dramatically, in the developing Drosophila brain (Li et al., 2017).”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites Briggs et al., 2017 source
    • cites Li et al., 2017

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • May combine two claims.

    Premisecitation

    OPCs are derived from neural tube precursors that are patterned along the anteroposterior axis; this has been demonstrated by genetic lineage tracing of Emx1-positive neural progenitors, which selectively labels forebrain oligodendrocytes.

    “OPCs are derived from neural tube precursors that are patterned along the anteroposterior axis. This has been demonstrated clearly, e.g., by genetic lineage tracing of Emx1-positive neural progenitors, which selectively labels forebrain oligodendrocytes (Kessaris et al., 2006).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Kessaris et al., 2006 source

      The Results (‘Subsequent waves of OLPs from the LGE/CGE and cortex’) report Emx1-Cre lineage tracing that labels oligodendrocyte precursors arising in the cortex, not throughout the forebrain. The Discussion describes region-specific forebrain precursor populations and a ventral-to-dorsal production sequence; it does not establish the claimed anteroposterior patterning through Emx1 tracing. (LLM, conf=0.88)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Premisecitation

    Abcg2 and Pgp encode drug and xenobiotic transporters known as BCGP and P-gp, respectively, which are expressed on barrier cells of the arachnoid mater of the meninges.

    “These two genes encode drug and xenobiotic transporters known as BCGP and P-gp, respectively, which are expressed on barrier cells of the arachnoid mater of the meninges (Yasuda et al., 2013).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Yasuda et al., 2013 source

      The Abstract and ‘Drug Transporters on Arachnoid Barrier Cells’ section report BCRP and P-gp expression in arachnoid barrier cells. The source links Abcg2 to BCRP, not ‘BCGP,’ and identifies the P-gp gene as Abcb1a, not ‘Pgp.’ (LLM, conf=0.87)

      Experimental — accuracy not yet measured

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

    Premisecitation

    Oligodendrocytes wrap myelin sheets around axons to support long-range neurotransmission and were previously analyzed by scRNA-seq.

    “Oligodendrocytes wrap myelin sheets around axons to support long-range neurotransmission and were previously analyzed by scRNA-seq (Marques et al., 2016).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Marques et al., 2016 source

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

    Premisecitation

    Ptgds was previously found as the most highly enriched gene in mouse leptomeninges.

    “the latter previously found as the most highly enriched gene in mouse leptomeninges (Yasuda et al., 2013)”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Yasuda et al., 2013 source

      Table 1 lists L-Ptgds with the highest mouse leptomeningeal microarray expression value among the genes shown, and the ‘Microarray Analysis of Drug Detoxification Genes in AB Leptomeninges’ section identifies prostaglandin D2 synthase as an arachnoid-barrier marker. The analysis covers selected genes; it does not establish that Ptgds was the most highly enriched gene across all mouse leptomeningeal genes. (LLM, conf=0.84)

      Experimental — accuracy not yet measured

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

    Study design and conductown data

    Although the oligodendrocyte lineage clusters aligned well with those previously published, there was not a perfect correspondence, and subtype labels in this paper do not correspond exactly to those previously described.

    “Note that although the oligodendrocyte lineage clusters aligned well with those previously published (Figure S1H; Marques et al., 2016), there was not a perfect correspondence, and subtype labels in this paper do not correspond exactly to those previously described.”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Marques et al., 2016 source

  • Classified as probably not a substantial claim.

    Interpretationcitation

    Since GLYT1 is a reversible glycine transporter, if it were expressed in telencephalic astrocytes, then those cells would potentially secrete glycine into the synaptic cleft instead of absorbing it.

    “We note that since GLYT1 is a reversible glycine transporter (Supplisson and Roux, 2002), if it were expressed in telencephalic astrocytes, then those cells would potentially secrete glycine into the synaptic cleft instead of absorbing it.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Supplisson and Roux, 2002 source

  • May combine two claims.

    Findingcitation

    Most olfactory neurons were GABAergic, and one was also dopaminergic.

    “Most olfactory neurons were GABAergic, in agreement with previous work (Nagayama et al., 2014), and one was also dopaminergic.”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Nagayama et al., 2014 source

      The Glomerular Layer section on periglomerular-cell neurotransmitters reports that GABAergic markers occur in more than half of juxtaglomerular cells. That supports the statement for this cell population, but not for olfactory neurons generally. The same section describes a dopamine-related subtype; it does not establish the citing authors’ observation that one neuron was also dopaminergic. (LLM, conf=0.86)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Findingcitation

    OPCs share many features of neural crest cells: they require the expression of Sox10 and Sox9, they are highly migratory, and they do not respect developmental borders in the brain.

    “Interestingly, however, OPCs share many features of neural crest cells: they require the expression of the two key transcription factors that specify neural crest (Sox10 and Sox9) (Takada et al., 2010), they are highly migratory, and they do not respect developmental borders in the brain.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Takada et al., 2010 source

      The Introduction and Discussion (page numbers unavailable) describe Sox9 as important for initial OPC specification and Sox10 as required for later oligodendrocyte survival or differentiation. They also report that OPC numbers recover in Sox9 mutants and remain normal in Sox10 mutants, so the unqualified claim that OPCs require both factors overstates the source. The citation is attached to the transcription-factor clause, not the subsequent claims about migration or developmental borders. (LLM, conf=0.88)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Findingown data

    248 (93%) of all clusters were uniquely identifiable with just two genes, 17 required three genes, and none required more than three.

    “Remarkably, we found that 248 (93%) of all clusters were uniquely identifiable with just two genes, while 17 required three genes and none required more than three”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The dataset was affected by technical artifacts including low-quality cells, batch effects, sex-specific gene expression, and neuronal-activity-dependent gene expression.

    “the dataset was affected by a number of technical artifacts, including low-quality cells, batch effects, sex-specific gene expression, neuronal-activity-dependent gene expression, and more.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Comparison with osmFISH from somatosensory cortex showed that interneurons were undersampled by scRNA-seq, likely due to their fragility, whereas astrocytes were undersampled by osmFISH due to difficulty of image segmentation.

    “Notably, interneurons were undersampled by scRNA-seq, likely due to their fragility, whereas astrocytes were undersampled by osmFISH due to the difficulty of image segmentation for irregularly shaped cells with small somata.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Codeluppi et al., 2018

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • May combine two claims.

    Findingown data

    In caudal regions, oligodendrocytes dominated, comprising 84% of cells in the hindbrain (excepting cerebellum) and 71% in the spinal cord.

    “comprising 84% of cells in the hindbrain (excepting cerebellum) and 71% in the spinal cord.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Neurons were most prevalent in rostral regions of the CNS, as well as in the cerebellum.

    “Neurons were most prevalent in rostral regions of the CNS, as well as in the cerebellum.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Although most neuronal types were already mature at the age investigated (postnatal days 20-30), signs of ongoing neurogenesis were observed in several regions.

    “Although most neuronal types were already mature at the age investigated (postnatal days 20–30), we observed signs of ongoing neurogenesis in several regions (Figure 2).”
    Quote in the paperSubstantial claim
    • Rests on an assumption: The adolescent age (postnatal days 20–30) is appropriate for identifying mature cell types and the overall architecture of the mouse nervous system.

  • May combine two claims.

    Findingown data

    Astrocytes, ependymal cells, and radial glia are developmentally related cell types and formed a subtree in the dendrogram.

    “Astrocytes, ependymal cells, and radial glia are developmentally related cell types and formed a subtree in the dendrogram (Figure 3).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Olfactory astrocytes were located around the olfactory glomeruli and could represent the previously described velate astrocytes, for which no molecular properties are known; they highly specifically expressed the Islr and Islr2 genes.

    “Olfactory astrocytes were located around the olfactory glomeruli and could represent the previously described velate astrocytes, for which no molecular properties are known; they highly specifically expressed the Islr and Islr2 genes encoding immunoglobulin-domain cell adhesion proteins (Figures 3 and S2), among other genes.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Enteric glia were very abundant in our dataset (91% of all enteric cells) and almost as diverse as enteric neurons, with seven distinct types.

    “Enteric glia were very abundant in our dataset (91% of all enteric cells) and almost as diverse as enteric neurons, with seven distinct types.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The radial glia-like cells (RGSZ and RGDG), which are the stem cells of both lineages, expressed Riiad1 (shared with ependymal cells) and were more similar to astrocytes than to any neuroblast.

    “The radial glia-like cells (RGSZ and RGDG), which are the stem cells of both lineages, expressed Riiad1 (shared with ependymal cells; Figure 2D) and were more similar to astrocytes than to any neuroblast.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    We observed distinct endothelial cell types carrying known arterial (e.g., Bmx; VECA) and venous (Slc38a5; VECV) markers, as well as capillary endothelial cells (VECC) expressing Meox1.

    “Like Vanlandewijck et al., we observed (Figure 5) distinct endothelial cell types carrying known arterial (e.g., Bmx; VECA) and venous (Slc38a5; VECV) markers, as well as capillary endothelial cells (VECC) expressing Meox1.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Vanlandewijck et al., 2018 source

  • May combine two claims.

    Findingown data

    In contrast to all other VLMC-like cell types, ABCs did not express Lum and showed only very low levels of Pdgfra.

    “In contrast to all other VLMC-like cell types, ABCs did not express Lum and showed only very low levels of Pdgfra.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The study observed seven molecularly distinct types of astrocytes with clear regionally specialized distribution.

    “Here, we observed seven molecularly distinct types of astrocytes with clear regionally specialized distribution.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    To test this hypothesis, the study examined expression of region-specific neural tube patterning genes Foxg1 (telencephalon), En1 and Pax3 (midbrain), and Hoxc6 (spinal cord); each of these genes marked the expected subset of astrocyte and ependymal cell types.

    “In order to test this hypothesis, we examined the expression of region-specific neural tube patterning genes, the transcription factors Foxg1 (telencephalon), En1, and Pax3 (midbrain) and Hoxc6 (spinal cord). Each of these genes marked the expected subset of astrocyte and ependymal cell types (Figure 3G).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    OPCs remained a single cluster, with only a distinction between cycling and non-cycling OPCs.

    “Furthermore, OPCs remained a single cluster, with only a distinction between cycling and non-cycling OPCs (Figures 4A and 4B).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Telencephalon astrocytes ACTE1 and ACTE2 were distinguished by expression of several genes, including Mfge8 and Lhx2, and were found in the olfactory bulb, cerebral cortex, striatum, amygdala, and hippocampus but were absent from the hypothalamus, thalamus, midbrain, and hindbrain.

    “Telencephalon astrocytes ACTE1 and ACTE2 were distinguished by the expression of several genes, including Mfge8 and Lhx2, and were found in the olfactory bulb, cerebral cortex, striatum, amygdala, and hippocampus but were absent from the hypothalamus, thalamus, midbrain, and hindbrain.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Non-telencephalic astrocytes ACNT1 and ACNT2 showed the opposite distribution, marked by Agt, and were found in all regions caudal to the telencephalon/diencephalon border.

    “Non-telencephalic astrocytes ACNT1 and ACNT2 showed the opposite distribution, marked by Agt (Angiotensinogen) and found in all regions caudal to the telencephalon/diencephalon border (i.e., posterior to and including the hypothalamus and thalamus).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In addition to Bergmann glia of the cerebellum (ACBG), the study found olfactory-specific astrocytes (ACOB), two subtypes of telencephalon-specific astrocytes (ACTE1 and ACTE2), two subtypes of non-telencephalon astrocytes (ACNT1 and ACNT2), and a Myoc-expressing astrocyte of the dorsal midbrain (ACMB).

    “In addition to Bergmann glia of the cerebellum (ACBG), we found olfactory-specific astrocytes (ACOB, unrelated to olfactory ensheathing cells; see below), two subtypes of telencephalon-specific astrocytes (ACTE1 and ACTE2), two subtypes of non-telencephalon astrocytes (ACNT1 and ACNT2), and a Myoc-expressing astrocyte of the dorsal midbrain, ACMB.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Similarly, Hox genes 1-5 were expressed in the hindbrain and spinal cord oligodendrocytes, remained expressed into mature oligodendrocytes, and were expressed at levels similar to those in neurons and astrocytes.

    “Similarly, we found that Hox genes 1–5 (that is, Hoxa1, Hoxb1, …, Hoxc5) were expressed in the hindbrain and spinal cord oligodendrocytes, remained expressed into mature oligodendrocytes, and were expressed at levels similar to those in neurons and astrocytes.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In contrast, several transcription factors responsible for patterning the forebrain and midbrain were detected only at very low levels (<1% of cells) if at all and did not appear in mature oligodendrocytes.

    “In contrast, several transcription factors responsible for patterning the forebrain and midbrain were detected only at very low levels (<1% of cells) if at all and did not appear in mature oligodendrocytes.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The first neuroblast category expressed Igfbpl1 and was either GABAergic (OBNBL3) or did not express any clear neurotransmitter phenotype; these were found in the rostral migratory stream (SZNBL and OBNBL3), dentate gyrus (DGNBL2), and habenula (DETPH).

    “The first category expressed Igfbpl1 and was either GABAergic (OBNBL3) or did not express any clear neurotransmitter phenotype. These neuroblasts were found in the rostral migratory stream (SZNBL and OBNBL3), dentate gyrus (DGNBL2), and habenula (DETPH).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The study did not observe distinct spinal cord populations corresponding to those previously described in the embryonic spinal cord; those astrocytes were described as dorsoventrally patterned and distinguished by combinatorial expression of Reln and Slit1, but to our knowledge, they have not been more extensively characterized molecularly or at postnatal stages.

    “We also did not observe distinct spinal cord populations corresponding to those previously described in the embryonic spinal cord (Hochstim et al., 2008). Those astrocytes were described as dorsoventrally patterned and distinguished by combinatorial expression of Reln and Slit1, but to our knowledge, they have not been more extensively characterized molecularly or at postnatal stages.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Hochstim et al., 2008 source

  • May combine two claims.

    Findingown data

    The second neuroblast category expressed Eomes and Slc17a7 and was glutamatergic; these were found in the olfactory bulb (OBNBL1, OBNBL2), cerebellum (CBNBL), and septum (SEPNBL).

    “The second category expressed the T-box transcription factor Eomes (also known as Tbr2) and the vesicular glutamate transporter (Slc17a7, also known as VGLUT1) and thus was glutamatergic. These neuroblasts were found in the olfactory bulb (OBNBL1, OBNBL2), cerebellum (CBNBL), and septum (SEPNBL).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In the spinal cord, the study detected clear expression of Hox genes 6-10, which are responsible for patterning the thoracic spinal cord; these genes were expressed in spinal cord oligodendrocytes only, at levels similar to those observed in neurons and astrocytes, and they remained expressed throughout the oligodendrocyte lineage.

    “In the spinal cord, we detected a clear expression of Hox genes 6–10 (that is, Hoxa6, Hoxb6, …, Hoxd10), which are responsible for patterning the thoracic spinal cord. These genes were expressed in spinal cord oligodendrocytes only, at levels similar to those observed in neurons and astrocytes, and they remained expressed throughout the oligodendrocyte lineage.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: Hox genes 6–10 are responsible for patterning the thoracic spinal cord.

  • May combine two claims.

    Findingown data

    The fourth VLMC-like cell type (ENMFBs) expressed all the VLMC marker genes but was found exclusively in the enteric nervous system.

    “The fourth VLMC-like cell type (enteric mesothelial fibroblasts; ENMFBs) expressed all the VLMC marker genes but was found exclusively in the enteric nervous system.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    We found three types of pericytes and a single arterial vascular smooth muscle type (Acta2, Tagln; VSMCA).

    “We found three types of pericytes and a single arterial vascular smooth muscle type (Acta2, Tagln; VSMCA).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The study confirmed induction of the key transcription factor Sox10 in OPCs and of the myelin oligodendrocyte glycoprotein Mog in COPs.

    “We confirmed induction of the key transcription factor Sox10 in OPCs and of the myelin oligodendrocyte glycoprotein Mog in COPs.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Schwann cells differ from CNS oligodendrocytes by expressing myelin components Pmp22 and Mpz, the tetraspanin Cd9, and Sparc and by not expressing Cldn11, Mobp, Mog, and Trf genes.

    “Schwann cells are the myelinating glia of the PNS and differ from CNS oligodendrocytes by expressing myelin components Pmp22 and Mpz, the tetraspanin Cd9, and the extracellular matrix calcium-binding osteonectin Sparc and by not expressing the tight junction Cldn11, the myelin protein Mobp, Mog, and the iron chelator Trf genes (Figure S3C).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The cerebral cortex was the most diverse, with 20 projection cell types, which were glutamatergic (all VGLUT1, but some additionally VGLUT2 or VGLUT3).

    “The cerebral cortex was the most diverse, with 20 projection cell types, which were glutamatergic (all VGLUT1, but some additionally VGLUT2 or VGLUT3).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The thalamic inhibitory neurons expressed Meis2 and shared key transcription factors (e.g., Dlx1, Dlx2, Dlx5, Dlx6) with other cell types in this taxon, as well as with striatum MSNs.

    “The thalamic inhibitory neurons expressed Meis2 and shared key transcription factors (e.g., Dlx1, Dlx2, Dlx5, Dlx6) with other cell types in this taxon, as well as with striatum MSNs, consistent with a common developmental origin in the ganglionic eminences.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In the ventral midbrain, we identified two types of dopaminergic neurons, one cholinergic and four GABAergic.

    “In the ventral midbrain, we identified two types of dopaminergic neurons, one cholinergic and four GABAergic.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    We identified six cell types in the cerebellum, of which five are previously known.

    “We identified six cell types in the cerebellum, of which five are previously known: Purkinje cells, granular cells, granular layer interneurons, molecular layer interneurons, and granular cell neuroblasts.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Nitric oxide was detected throughout the nervous system and did not combine preferentially with or avoid any other neurotransmitter.

    “The gaseous neurotransmitter nitric oxide (i.e., Nos1 expression) was detected throughout the nervous system and did not combine preferentially with (or avoid) any other neurotransmitter (Figures 1C and S6A).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    A sixth cell type (MEINH1) was found in the midbrain but was molecularly indistinguishable from cerebellum molecular layer interneurons (CBINH1).

    “A sixth cell type (MEINH1), curiously, was found in the midbrain but was molecularly indistinguishable (Figure S1E) from cerebellum molecular layer interneurons (CBINH1).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Spinal cord cell types expressed Hoxa1 through Hoxd10, with additional expression of lumbar Hox genes in some cell types.

    “For example, spinal cord cell types expressed Hoxa1 (rhombomere 1) through Hoxd10 (thoracic bordering on lumbar), with additional expression of lumbar Hox genes in some cell types.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Acetylcholine occurred with most other neurotransmitters, whereas serotonin occurred only alone or with VGLUT3 or GABA.

    “Acetylcholine occurred with most other neurotransmitters, whereas, for example, serotonin occurred only alone or with VGLUT3 or GABA.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    In the hindbrain, all inhibitory neurons were glycinergic, and excitatory neurons were a mix of VGLUT1 and VGLUT2.

    “In the hindbrain (15 types not including cerebellum), all inhibitory neurons were glycinergic (GLYT1, GLYT2, or both), and excitatory neurons were a mix of VGLUT1 and VGLUT2.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    We found 38 excitatory and inhibitory cell types of the diencephalon and midbrain, forming a unified taxon.

    “We further found 38 excitatory and inhibitory cell types of the diencephalon (thalamus and hypothalamus) and midbrain, forming a unified taxon.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Glutamate (VGLUT2) was the only neurotransmitter expressed in all compartments, while GABA contributed the larger number of cell types and was mostly concentrated in the forebrain.

    “While glutamate (VGLUT2) was the only neurotransmitter expressed in all compartments, GABA contributed the larger number of cell types and was mostly concentrated in the forebrain.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    VGLUT3 was often co-expressed with cholinergic and monoaminergic neurotransmitters and more rarely alone or with the other VGLUTs or GABA.

    “In contrast, the atypical vesicular glutamate transporter VGLUT3 was often co-expressed (Figures 1C and S6A) with cholinergic and monoaminergic neurotransmitters and more rarely alone or with the other VGLUTs or GABA.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In the spinal cord, we identified 22 cell types, split into inhibitory (GABAergic or glycinergic) and glutamatergic (VGLUT2).

    “Finally, in the spinal cord, we identified 22 cell types, again split into inhibitory (GABAergic or glycinergic) and glutamatergic (VGLUT2) in good agreement with an independent experiment focused on the dorsal horn (Häring et al., 2018) (Table S2).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Häring et al., 2018 source

  • May combine two claims.

    Findingown data

    We found putative patch-specific D1-/D2-type neurons (expressing Tshz1) and matrix-specific D2 neurons (expressing Gng2).

    “In addition, we found putative patch-specific D1-/D2-type neurons (expressing Tshz1) and matrix-specific D2 neurons (expressing Gng2), consistent with staining patterns of these genes in the Allen Mouse Brain Atlas.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Somatostatin (Sst) is a canonical marker of inhibitory neuronal subtypes in the forebrain but was widely expressed in excitatory neurons in the spinal cord, hindbrain, and di-mesencephalon.

    “For example, somatostatin (Sst) is a canonical marker of inhibitory neuronal subtypes in the forebrain but was widely expressed in excitatory neurons in the spinal cord, hindbrain, and di-mesencephalon.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    We found two D1-type MSNs (MSN1 and MSN4), one enriched in dorsal and one in ventral striatum, as well as two D2-type MSNs (MSN2 and MSN3), also dorsal and ventral.

    “We found two D1-type MSNs (MSN1 and MSN4), one enriched in dorsal and one in ventral striatum, as well as two D2-type MSNs (MSN2 and MSN3), also dorsal and ventral, demonstrating a molecular distinction corresponding to the distinct circuits and functions of dorsal and ventral MSNs.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    These types segregated nearly perfectly into glutamatergic (mostly VGLUT1) and GABAergic subsets but included two cholinergic types.

    “These types segregated nearly perfectly into glutamatergic (mostly VGLUT1) and GABAergic subsets but included two cholinergic types (of the red nucleus and the habenula).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Telencephalic inhibitory interneurons formed a separate taxon, with the olfactory cells as a distinct subgroup.

    “Telencephalic inhibitory interneurons, including cells from the olfactory bulb, cortex, hippocampus, and thalamus, formed a separate taxon, with the olfactory cells as a distinct subgroup.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Neurons of the PNS segregated molecularly from the CNS and formed distinct sensory, sympathetic, and enteric subdivisions.

    “Neurons of the PNS segregated molecularly from the CNS and formed distinct sensory, sympathetic, and enteric subdivisions (Figures 1C and S4).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The nitrergic ENT1-3 expressed the high-affinity choline transporter Slc5a7, but Chat was very low or undetected in those neurons.

    “The nitrergic ENT1-3 expressed the high-affinity choline transporter Slc5a7, but Chat was very low or undetected in those neurons.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    A single taxon collected nearly all cholinergic, monoaminergic neurons from the whole brain, as well as peptidergic neurons mainly of the hypothalamus.

    “A single taxon collected nearly all cholinergic, monoaminergic neurons (which we identified based on expression of the necessary biosynthesis enzymes and vesicular and reuptake transporters; Figure S6C and STAR Methods) from the whole brain, as well as peptidergic neurons mainly of the hypothalamus.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingnone given

    They retained their CNS neuron character and did not intermingle with cholinergic or monoaminergic neurons of the PNS.

    “On the other hand, they still retained their CNS neuron character and did not intermingle with cholinergic or monoaminergic neurons of the PNS.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Glutamatergic neurons in the telencephalon all used VGLUT1, with some additionally using VGLUT2, whereas in more caudal regions, VGLUT2 dominated.

    “Glutamatergic neurons in the telencephalon all used VGLUT1, with some additionally using VGLUT2, whereas in more caudal regions, VGLUT2 dominated.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Pyramidal neurons of the piriform and entorhinal cortex, as well as the subiculum, were molecularly closely related and spatially aligned.

    “For example, pyramidal neurons of the piriform and entorhinal cortex, as well as the subiculum, were molecularly closely related (shown by their forming a separate subtree of the dendrogram), as well as spatially aligned.”
    Quote in the paperNot a substantial claim

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

    Findingown data

    At level 3, some clusters remained suspected doublets, and some over-split clusters lacked clearly defining gene expression differences.

    “Despite our efforts, at level 3 there remained still some clusters that were suspected doublets, as well as over-split clusters that lacked clearly defining gene expression differences.”
    Quote in the paperNot a substantial claim

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

    Findingown data

    In the dendrogram without gene exclusion, olfactory bulb inhibitory neurons were placed next to the MSNs.

    “Second, the olfactory bulb inhibitory neurons were placed next to the MSNs.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Foxg1 was found in all forebrain neurons, as well as in telencephalon-specific astrocytes.

    “For example, the forebrain patterning gene Foxg1 was found in all forebrain neurons, as well as in telencephalon-specific astrocytes.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Findingown data

    Dropping non-significant principal components reduced the gene expression space to a few tens of dimensions, typically about forty.

    “Dropping non-significant principal components (Kolmogorov-Smirnov test, p < 0.05) reduced the space to a few tens of dimensions (typically about forty).”
    Quote in the paperSubstantial claim

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

    Findingown data

    Clusters CBPC, HYPEP3 and SCINH2 showed dual presence of GABA (inhibitory) and glutamate (excitatory) in the same cluster.

    “Clusters CBPC, HYPEP3 and SCINH2 showed dual presence of GABA (inhibitory) and glutamate (excitatory) in the same cluster”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingreasoning

    The territories defining these gene expression domains corresponded closely to those marked out by embryonic morphogens, and spatial differences in adult expression patterns correlated with persistent expression of developmental transcription factors.

    “The territories defining these gene expression domains corresponded closely to those marked out by embryonic morphogens, and spatial differences in adult expression patterns correlated with persistent expression of developmental transcription factors.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    This trend was strongest among neurons, astrocytes, and ependymal cells; by contrast, oligodendrocytes, vascular cells, and immune cells exhibited similar gene expression patterns across brain regions.

    “This trend was strongest among neurons, astrocytes, and ependymal cells; by contrast, oligodendrocytes, vascular cells, and immune cells exhibited similar gene expression patterns across brain regions.”
    Quote in the paperSubstantial claim

  • The quote only partly states this claim.

    Findingown data

    Manual inspection indicated GABA in clusters OBINH4, SZNBL and DEINH6.

    “but manual inspection indicated GABA.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Based on criterion (2), more than 50% of the 264 branches had probability of 1 and about 85% had probability greater than 0.5.

    “Based on the more stringent criterion (2) more than 50% had probability of 1 and about 85% greater than 0.5.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingreasoning

    Neurons share an extensive gene program involving synaptic, cytoskeletal, and ion channel genes, while oligodendrocytes express gene programs required for generating myelin.

    “For example, neurons share an extensive gene program involving synaptic, cytoskeletal, and ion channel genes, while oligodendrocytes express gene programs required for generating myelin.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingreasoning

    Specificity tends to increase as the gene set becomes more selective, but then decrease as it becomes less robust.

    “Specificity tends to increase as the gene set becomes more selective, but then decrease as it becomes less robust.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Based on criterion (1), more than 65% of the 264 branches had probability of 1 and 94% had probability greater than 0.5.

    “More than 65% of the 264 branches had probability of 1 and 94% had probability greater than 0.5 based on criterion (1).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Generally, robustness drops as more genes are added, while selectivity increases.

    “Generally, robustness drops as more genes are added, while selectivity increases.”
    Quote in the paperNot a substantial claim

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

    Findingown data

    Some preliminary clusters were clearly derived from doublets, expressing contradictory markers from different major classes, such as neurons and vascular cells.

    “Some clusters were also clearly derived from doublets, expressing contradictory markers e.g., from neurons and vascular cells.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Dorsoventral patterning was preserved: Emx1 was expressed in cortical, hippocampal, and striatal projection neurons, whereas Dlx1 and Dlx5 were found mainly in inhibitory neurons of the same tissues.

    “Dorsoventral patterning was also preserved: the dorsal gene Emx1 was expressed in cortical, hippocampal, and striatal projection neurons, whereas ventral Dlx1 and Dlx5 were found mainly in inhibitory neurons of the same tissues.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Projecting the multiscale KNN graph with graph t-SNE resulted in a more accurate projection of the graph itself, with more compact and well-defined neighborhoods.

    “The result was a more accurate projection of the graph itself, with more compact and well-defined neighborhoods.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationreasoning

    Oligodendrocytes showed a loss of regional identity followed by a secondary diversification.

    “oligodendrocytes showed a loss of regional identity followed by a secondary diversification”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationnone given

    The clustering is highly conservative, and significant heterogeneity likely remains within many of the reported clusters.

    “This represents a highly conservative clustering, and significant heterogeneity likely remains within many of the reported clusters.”
    Quote in the paperNot a substantial claim

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

    Premisecitation

    The adult brain is organized into dorsoventral and rostrocaudal compartments, which result from patterning of the early neural tube.

    “The adult brain is organized into dorsoventral and rostrocaudal compartments, which result from patterning of the early neural tube (Rubenstein and Rakic, 2013).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Rubenstein and Rakic, 2013

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • Classified as probably not a substantial claim.

    Premisecitation

    The modern understanding of astrocyte diversity essentially stands as it stood in 1900: the major types of mature astrocytes are believed to be the Müller glia of the retina, the Bergmann glia of the cerebellum, and the widely distributed protoplasmic and fibrous astrocytes.

    “the modern understanding of astrocyte diversity essentially stands as it stood in 1900: the major types of mature astrocytes are believed to be the Müller glia of the retina, the Bergmann glia of the cerebellum, and the widely distributed protoplasmic and fibrous astrocytes (Ben Haim and Rowitch, 2017).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Ben Haim and Rowitch, 2017 source

  • May combine two claims.

    Interpretationreasoning

    Thus, an initially diverse population of neural progenitors converges on a single intermediate transcriptional state (OPC or COP) and is then subject to secondary diversification as they mature.

    “Thus, an initially diverse population of neural progenitors converges on a single intermediate transcriptional state (OPC or COP) and is then subject to secondary diversification as they mature (Figure 4E).”
    Quote in the paperSubstantial claim

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

    Interpretationreasoning

    This may explain the need for distinct types of astrocytes in glycine-rich and glycine-poor regions of the brain.

    “This may explain the need for distinct types of astrocytes in glycine-rich and glycine-poor regions of the brain.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationreasoning

    At such low levels of expression, it is difficult to rule out contamination from adjacent neurons, and thus it is possible that they were not expressed at all in the oligodendrocyte lineage.

    “At such low levels of expression, it is difficult to rule out a contamination from adjacent neurons, and thus, it is possible that they were not expressed at all in the oligodendrocyte lineage.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationown data

    The study concludes that OPCs (and, to a lesser extent, COPs and NFOLs) may retain a memory of their anteroposterior position in the form of expression of region-specific transcription factors but that this does not translate into clearly distinct region-specific cell types.

    “We conclude that OPCs (and, to a lesser extent, COPs and NFOLs) may retain a memory of their anteroposterior position in the form of expression of region-specific transcription factors but that this does not translate into clearly distinct region-specific cell types.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Study design and conductown data

    The study validated the identity and distribution of astrocyte cell types using RNA FISH (RNAscope), which was consistent with the Allen Mouse Brain Atlas.

    “We validated the identity and distribution of astrocyte cell types using RNA FISH (RNAscope), which was consistent with the Allen Mouse Brain Atlas (Figures 3F and S2).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    Eomes and Igfbpl1 overlapped in some populations (DGNBL1 and to some extent SZNBL), indicating that these categories of neuroblasts may represent sequential stages of neuronal maturation rather than divergent cell types.

    “However, Eomes and Igfbpl1 overlapped in some populations (DGNBL1 and to some extent SZNBL), indicating that these categories of neuroblasts may represent sequential stages of neuronal maturation rather than divergent cell types.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    VLMC-like cells are present throughout the body and are not brain specific.

    “This demonstrates that VLMC-like cells are present throughout the body and are not brain specific.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    These findings point to the specific functions that differ between neuronal types (connectivity, electrophysiology, and neurotransmission) and to the underlying regulatory machinery (transcription factors).

    “These findings point to the specific functions that differ between neuronal types (connectivity, electrophysiology, and neurotransmission) and to the underlying regulatory machinery (transcription factors).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    Neuropeptides, neurotransmitters, calcium-binding proteins, and other neuronal molecules are used in a highly modular fashion and serve different functions in different contexts.

    “These results demonstrate that neuropeptides, neurotransmitters, calcium-binding proteins, and other neuronal molecules are used in a highly modular fashion and serve different functions in different contexts.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Interpretationnone given

    This layer order corresponds with their order of development during embryogenesis.

    “Notably, this also corresponds with their order of development during embryogenesis.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    Olfactory ensheathing cells are neural-crest-derived cells that ensheath axons of the olfactory sensory neurons but do not form myelin.

    “Olfactory ensheathing cells are neural-crest-derived (Barraud et al., 2010) cells that ensheath axons of the olfactory sensory neurons but do not form myelin.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Barraud et al., 2010 source

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

    Premisecitation

    Approximately ten cell types have been previously described in the myenteric plexus of the mouse.

    “Based on marker gene expression, morphology, location, and projection targets, approximately ten cell types have been previously described (Furness et al., 2014, Qu et al., 2008) in the myenteric plexus of the mouse.”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Furness et al., 2014 source
    • cites Qu et al., 2008

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • May combine two claims.

    Study design and conductown data

    For neurons, the classifier had precision 93% and recall 99%: 99% of all neurons were classified correctly, and 93% of all cells classified as neurons were actually neurons.

    “The precision and recall for neurons was 93% and 99%, respectively. That is, 99% of all neurons were classified correctly, and 93% of all cells classified as neurons were actually neurons.”
    Quote in the paperSubstantial claim

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

    Interpretationnone given

    The actual genome-wide FDR will be strictly equal to or lower than PEP when PEP is applied individually to each gene.

    “Note that PEP is applied individually to each gene (hence, ‘local FDR’) and the actual genome-wide FDR will be strictly equal to or lower than PEP.”
    Quote in the paperNot a substantial claim
    • The authors state this as an assumption: The trinarization model applies to a cluster of cells representing a putatively homogeneous population.

  • May combine two claims.

    Study design and conductown data

    The study had technical and experimental limitations including doublets, sex-specific gene expression, and low-quality cells.

    “First, there were technical and experimental limitations as detailed above, including doublets, sex-specific gene expression, and low-quality cells.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationreasoning

    A secondary diversification, more graded and less region specific, results from interaction with the local environment and likely reflects inducible gene regulatory networks that respond in graded and transient fashion to local molecular cues.

    “Third, a secondary diversification, more graded and less region specific, results from interaction with the local environment and likely reflects inducible gene regulatory networks that respond in graded and transient fashion to local molecular cues.”
    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

    We performed a very conservative clustering, designed to reveal clearly distinct major cell types, but did not analyze the substantial remaining heterogeneity within clusters.

    “Fourth, we have performed a very conservative clustering, designed to reveal clearly distinct major cell types, but did not analyze the substantial remaining heterogeneity within clusters.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing). May combine two claims.

    Study design and conductown data

    We have described only molecular cell types, but the task of linking molecular properties to functional, anatomical, morphological, and electrophysiological properties remains.

    “Finally, we have described only molecular cell types, but the task of linking molecular properties to functional, anatomical, morphological, and electrophysiological properties remains.”
    Quote in the paperNot a substantial claim

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

    Interpretationreasoning

    Cycling cells shared most gene expression with their non-cycling counterparts, which presumably caused the classifier difficulty.

    “presumably because they shared most gene expression with their non-cycling counterparts”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationnone given

    Multiple levels of hierarchical subdivision exist within these classes; within neurons, neurotransmitter phenotype showed a modular and highly regulated pattern of expression.

    “Multiple levels of hierarchical subdivision exist within these classes; for example, within neurons, neurotransmitter phenotype showed a modular and highly regulated pattern of expression.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S4 (based).

    Interpretationnone given

    Batch effects were mainly due to ambient oligodendrocyte RNA in hindbrain and spinal cord samples.

    “In order to suppress batch effects (mainly due to ambient oligodenderocyte RNA in hindbrain and spinal cord samples), we collected the unique set of genes pan-enriched in the non-neuronal clusters”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationreasoning

    In the dendrogram without gene exclusion, enteric neurons clustered together with enteric glia, probably due to enteric glia being extremely abundant in the tissue.

    “First, enteric neurons clustered together with the enteric glia probably due to fact that enteric glia were extremely abundant in the tissue.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationreasoning

    Transcription factor networks induced in early development by local morphogens result in heritable regulatory states, which in turn are relayed into the diversification of terminal neuronal and astrocytic types specific to each brain region.

    “This suggests that transcription factor networks induced in early development by local morphogens result in heritable regulatory states, which in turn are relayed into the diversification of terminal neuronal and astrocytic types specific to each brain region.”
    Quote in the paperSubstantial claim

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

    Interpretationreasoning

    Purkinje cells were likely undersampled here due to their size.

    “Third, some cell types may have been lost to differential survival or size selection biases (for example, Purkinje cells were likely undersampled here due to their size).”
    Quote in the paperNot a substantial claim

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

    Study design and conductnone given

    We used relatively shallow sequencing.

    “Similarly, we used relatively shallow sequencing, and deeper sequencing using more sensitive RNA-seq methods is likely to resolve more subtypes.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationown data

    The dendrogram constructed without any gene exclusion was not fundamentally changed from Figure 1C, but included a few key differences which the authors believe are technical artifacts.

    “The resulting dendrogram was not fundamentally changed from Figure 1C, but included a few key differences which we believe are technical artifacts.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationreasoning

    Oligodendrocytes did not show similar spatial patterns, revealing a loss of regional patterning in the oligodendrocyte lineage.

    “The fact that oligodendrocytes did not show similar spatial patterns—despite being derived from the same initially patterned neural tube as neurons and astocytes—reveals a loss of regional patterning in the oligodendrocyte lineage, presumably because region-specific patterning is transient and not converted to permanent states in these lineages.”
    Quote in the paperSubstantial claim

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

    Interpretationreasoning

    In the dendrogram without gene exclusion, the OPC cluster was placed next to the SZNBL cluster, probably because of strong cell-cycle signal.

    “Finally, the OPC cluster was placed next to the SZNBL cluster probably because of strong cell-cycle signal.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationnone given

    The atlas can be used to identify genes and gene combinations unique to specific cell types, which can be used to genetically target cells for visualization, ablation, optogenetic manipulation, gene targeting, and more.

    “The atlas can be used to identify genes and gene combinations unique to specific cell types, which in turn can be used to genetically target cells for visualization, ablation, optogenetic manipulation, gene targeting, and more.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationreasoning

    This secondary diversification was observed most clearly in the oligodendrocyte lineage but likely occurs to some extent in all lineages.

    “This was observed most clearly in the oligodendrocyte lineage but likely occurs to some extent in all lineages.”
    Quote in the paperSubstantial claim

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

    Interpretationreasoning

    Deeper sequencing using more sensitive RNA-seq methods is likely to resolve more subtypes.

    “Similarly, we used relatively shallow sequencing, and deeper sequencing using more sensitive RNA-seq methods is likely to resolve more subtypes.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S2 (checkable). May combine two claims.

    Interpretationreasoning

    The atlas can lead to actionable hypotheses on the mechanism of disease and identify relevant cell types to generate mouse models of human disease.

    “This can lead to actionable hypotheses on the mechanism of disease, as well as identifying the relevant cell types to generate mouse models of human disease.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S4 (based).

    Interpretationnone given

    The diversity of gene expression patterns in the nervous system can be understood through three major principles.

    “We suggest that the diversity of gene expression patterns in the nervous system can be understood through three major principles.”
    Quote in the paperNot a substantial claim
116 of 116

  • The paper relies on this without support.

    The mouse nervous system is representative of the mammalian nervous system.

    “The resource presented here lays a solid foundation for understanding the molecular architecture of the mammalian nervous system”

  • The paper relies on this without support.

    The sampled regions and cell numbers are sufficient to capture the full diversity of cell types in the mouse nervous system.

    “In total, we analyzed 19 regions (Figure 1A) but omitted at least the retina, the olfactory epithelium, the vomeronasal organ, the inner ear, and the parasympathetic ganglia.”

  • The paper relies on this without support.

    The adolescent age (postnatal days 20–30) is appropriate for identifying mature cell types and the overall architecture of the mouse nervous system.

    “Although most neuronal types were already mature at the age investigated (postnatal days 20–30)”

  • The paper relies on this without support.

    The developmental origin assigned to each cluster (e.g., telencephalon, diencephalon, midbrain, hindbrain) is correct.

    “We assigned each cluster a unique mnemonic identifier (e.g., MBDOP1), descriptive name (“midbrain dopaminergic neuron”), major class (e.g., “neuron”), neurotransmitter identity, putative developmental origin, anatomical location, and region (Table S3).”

  • The paper relies on this without support.

    OPCs are the progenitors of the entire oligodendrocyte lineage.

    “Since OPCs are the progenitors of the entire oligodendrocyte lineage”

  • The paper relies on this without support.

    Hox genes 6–10 are responsible for patterning the thoracic spinal cord.

    “Hox genes 6–10 (that is, Hoxa6, Hoxb6, …, Hoxd10), which are responsible for patterning the thoracic spinal cord.”

  • The paper relies on this without support.

    Glycine is a widely used inhibitory neurotransmitter only in the caudal parts of the brain and in the spinal cord.

    “Glycine is a widely used inhibitory neurotransmitter only in the caudal parts of the brain and in the spinal cord.”

  • The paper relies on this without support.

    The dendrogram based on gene expression distance reflects true cell type relationships.

    “we calculated a robust dendrogram of cell types (Figure 1C and STAR Methods), showing relationships between cell types based on gene expression distance.”

  • The paper relies on this without support.

    The technical artifacts can be sufficiently mitigated by the cytograph pipeline so that the resulting clusters reflect biological cell types.

    “we developed a multistage analysis pipeline called “cytograph,” which progressively discovers cell types or states while mitigating the impact of technical artifacts”

  • The authors state this as an assumption.

    OPCs are produced by the same progenitors as astrocytes and neurons.

    “OPCs are derived from the neural tube and assumed to be produced by the same progenitors as astrocytes and neurons.”

  • The paper relies on this without support.

    The enteric nervous system has not been previously studied in molecular detail using single-cell methods.

    “The enteric nervous system has not been previously studied in molecular detail using single-cell methods.”

  • The paper relies on this without support.

    The diversity and function of enteric glia are not known in detail.

    “The diversity and function of enteric glia are not known in detail.”

  • The paper relies on this without support.

    Synaptic connectivity, neurotransmission, and membrane conductance are uniquely neuronal properties.

    “But synaptic connectivity, neurotransmission, and membrane conductance are uniquely neuronal properties”

  • The paper relies on this without support.

    Some resolution limit-free algorithms can be tuned to detect smaller clusters, but at the expense of breaking up large clusters.

    “Some variants (so called resolution limit-free algorithms) can be tuned to detect smaller clusters, but at the expense of breaking up large clusters.”

  • The paper relies on this without support.

    Granule cells of the dentate gyrus and the cerebellum are not related.

    “Note: we pooled granule cells of the dentate gyrus and the cerebellum not because we think they are related (they are not), but because they are both extremely abundant and tended to skew manifold learning when included with other cells.”

  • The paper relies on this without support.

    Many, even most, of the cell types described in this paper were not previously associated with known markers.

    “Many, even most, of the cell types described in this paper were not previously associated with known makers.”

  • The authors state this as an assumption.

    The trinarization model applies to a cluster of cells representing a putatively homogeneous population.

    “The model applies to a cluster of cells representing a putatively homogeneous population.”
17 of 17

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?

  • VLMC types show highly specific spatial and colocalization patterns.

    “VLMC types66,82 also show highly specific spatial and colocalization patterns.”

    From A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain (2023) · cites this paper as [66]

    The Results section, “Vascular Cells and a Family of Broadly Distributed Mesothelial Fibroblasts” (page unavailable), identifies distinct VLMC-like types and reports specific locations, including enteric mesothelial fibroblasts found exclusively in the enteric nervous system. It does not establish highly specific colocalization patterns for VLMC types, so that part of the claim is unsupported. (LLM, conf=0.82)

    Experimental — accuracy not yet measured

  • At finer resolution, DNA damage signals tend to be enriched in H3K27ac peak regions, with highest enrichment in neurons and non-neuronal brain cell types (including ODC and MiG), and weak enrichment in Endo and VLMCs.

    “At a finer resolution, DNA damage signals again tend to be enriched in H3K27ac peak regions: neurons and non-neuronal brain cell types (including ODC and MiG cells) showing the highest enrichment; while Endo and VLMCs, which are not brain-specific cell types display weak enrichments64”

    From Single-cell parallel analysis of DNA damage and transcriptome reveals selective genome vulnerability (2025) · cites this paper as [64]

    The Results section, “Vascular Cells and a Family of Broadly Distributed Mesothelial Fibroblasts” (page unavailable), says VLMC-like cells are not brain-specific, supporting that limited part of the sentence. The cited paper’s passages do not report DNA-damage signals in H3K27ac peaks or compare their enrichment across neurons, ODC, MiG, Endo, and VLMCs. (LLM, conf=0.82)

    Experimental — accuracy not yet measured

  • Organoid neurons were reminiscent of NC-derived neurons found in cranial or dorsal root ganglia, with medium-large soma NEFH+PRPH+ neurons and smaller soma NEFH−PRPH+ neurons.

    “The organoid neurons were reminiscent of NC-derived neurons found in cranial or dorsal root ganglia, with medium-large soma Neurofilament-Heavy Chain (NEFH)+ Peripherin (PRPH)+ neurons and smaller soma NEFH−PRPH+ neurons (Fig. 3o, Supplementary Video 7)23,31.”

    From Hair-bearing human skin generated entirely from pluripotent stem cells (2020) · cites this paper as [23]

    The Results section, “Peripheral Nervous System” (page unavailable), identifies dorsal-root-ganglion sensory neurons and a neurofilament branch, supporting part of the comparison. It does not describe the claimed NEFH/PRPH combinations or their association with medium-large versus smaller somata, nor does it establish the comparison with cranial ganglion neurons. The organoid observations are presented as the citing authors’ own results, not as findings of this source. (LLM, conf=0.83)

    Experimental — accuracy not yet measured

  • Less is known about the transcriptomic heterogeneity of astrocytes across different cortical areas in the aging human brain.

    “but less is known about the transcriptomic heterogeneity of astrocytes across different cortical areas in the aging human brain.”

    From Astrocyte transcriptomic changes along the spatiotemporal progression of Alzheimer’s disease (2024) · cites this paper as [29]

    The Results section, “Astroependymal Cells Are Diverse and Spatially Patterned” (page not provided), describes limited historical understanding of astrocyte diversity and identifies regionally distinct astrocytes in mice. It does not assess how much is known about transcriptomic differences across cortical areas in the aging human brain. (LLM, conf=0.76)

    Experimental — accuracy not yet measured

  • These observations are consistent with the notion that astrocytes and neurons are derived from common regionally distinct progenitors and share common transcription factors for spatial patterning.

    “These observations are consistent with the notion that astrocytes and neurons are derived from common regionally distinct progenitors and share common transcription factors for spatial patterning66,67.”

    From A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain (2023) · cites this paper as [66]

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • Sixth purported cerebellar cell type was found in the midbrain

    Minor

    The paper counts six cell types in the cerebellum, but locates its sixth type, MEINH1, in the midbrain. It also says MEINH1 is molecularly indistinguishable from a cerebellar type already among the five listed.

1 of 1

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Authors
Zeisel, A., Hochgerner, H., Lönnerberg, P., Johnsson, A., Memic, F., van der Zwan, J., Häring, M., Braun, E., Borm, L. E., La Manno, G., Codeluppi, S., Furlan, A., Lee, K., Skene, N., Harris, K. D., Hjerling-Leffler, J., Arenas, E., Ernfors, P., Marklund, U., & Linnarsson, S.
Affiliations
  • Karolinska Institutet (SE)
  • UCL Queen Square Institute of Neurology (GB)
Corresponding author
Linnarsson, Sten
ORCID
Venue
Cell
Publisher
Elsevier BV
Published
2018-08
Volume
174
Issue
4
Pages
999-1014.e22
ISSN
0092-8674 (ISSN-L)
DOI
10.1016/j.cell.2018.06.021
PMC
PMC6086934
OpenAlex
W2949693884
Cited by
2,995
References
53
Citations by year
2026: 197 · 2025: 327 · 2024: 322 · 2023: 361 · 2022: 388 · 2021: 416 · 2020: 379 · 2019: 209 · 2018: 45
FWCI
95.79
Type
journal article
Language
en
Open access
Licence
Locations
  • Cell (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
  • PubMed (publishedVersion)
  • Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (acceptedVersion)
  • Europe PMC (PubMed Central) (submittedVersion, cc-by)
  • PubMed Central (submittedVersion, cc-by)
  • UCL Discovery (University College London) (submittedVersion)
  • Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion, cc-by-nc-nd)
  • Spiral (Imperial College London) (submittedVersion, cc-by)
Funders
  • Knut and Alice Wallenberg Foundation (2015.0041)
  • Swedish Foundation for Strategic Research (SSF (RIF 14-0057, SB16-0065)
  • Wellcome Trust (108726/Z/15/Z)
  • Swedish Research Council (2016-01526, 2016-03130)
  • SSF (SRL, SB16-0065)
  • Cancerfonden (CAN 2016/572)
  • EU
  • Hjärnfonden (FO2017-0059)
  • SFO Strat Regen (SG-2018)
  • European Research Council (740491)
  • Ollie and Elof Ericssons Foundation
  • Åke Wiberg Foundation (M16-0197)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
  • Life Sciences › Neuroscience › Developmental Neuroscience › Neurogenesis and neuroplasticity mechanisms
  • Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Neuroscience and Neuropharmacology Research
Keywords
single-cell transcriptomics, neuronal heterogeneity, astrocyte heterogeneity, neurotransmitters, neuropeptides, glutamate, glycine, synaptic connectivity
MeSH terms
Animals, Female, Male, Mice, Inbred C57BL, Nervous System, Gene Expression Regulation, Developmental

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.

Cited sources are checked by gpt-6-sol.

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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