The DOI matches its Crossref record; 47 of the 47 references it cites were found in a registry or an index; 1 of the 24 sources its claims cite were checked for support.
Developmental diversification of cortical inhibitory interneurons
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Abstract
Diverse subsets of cortical interneurons have vital roles in higher-order brain functions. To investigate how this diversity is generated, here we used single-cell RNA sequencing to profile the transcriptomes of mouse cells collected along a developmental time course. Heterogeneity within mitotic progenitors in the ganglionic eminences is driven by a highly conserved maturation trajectory, alongside eminence-specific transcription factor expression that seeds the emergence of later diversity. Upon becoming postmitotic, progenitors diverge and differentiate into transcriptionally distinct states, including an interneuron precursor state. By integrating datasets across developmental time points, we identified shared sources of transcriptomic heterogeneity between adult interneurons and their precursors, and uncovered the embryonic emergence of cardinal interneuron subtypes. Our analysis revealed that the transcription factor Mef2c, which is linked to various neuropsychiatric and neurodevelopmental disorders, delineates early precursors of parvalbumin-expressing neurons, and is essential for their development. These findings shed new light on the molecular diversification of early inhibitory precursors, and identify gene modules that may influence the specification of human interneuron subtypes.
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57 Own result · 16 Not checked yet · 14 Own interpretation · 5 Own method · 1 Couldn’t confirm · 1 No basis given · accuracy not yet measured
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“Heterogeneity within mitotic progenitors in the ganglionic eminences is driven by a highly conserved maturation trajectory, alongside eminence-specific transcription factor expression that seeds the emergence of later diversity.”
- Also stated in: § Introduction · plain
“Within mitotic progenitors, we found a highly conserved maturation trajectory, accompanied by eminence-specific transcription factor expression that seeds the emergence of later cell diversity.”
§ Developmental diversification of cortical inhibitory interneurons > Abstract
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“Upon becoming postmitotic, progenitors diverge and differentiate into transcriptionally distinct states, including an interneuron precursor state.”
§ Developmental diversification of cortical inhibitory interneurons > Abstract
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“Our analysis revealed that the ASD-associated transcription factor Mef2c delineates early Pvalb-precursors, and is essential for their development.”
- Also stated in: § Diversity emerges from a common precursor state · plain
“the transcription factor Mef2c was among the genes discriminating early Pvalb-precursors from other MGE-derived interneuron types”
§ Developmental diversification of cortical inhibitory interneurons > Abstract
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“conditional deletion of Mef2c in inhibitory neurons led to a specific loss of Pvalb-interneurons by P20 in cortical layers 2-6”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Diversity emerges from a common precursor state
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“when we performed the unsupervised branching analysis only in mitotic progenitors, we found no evidence for the specification of distinct interneuron fates”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Transcriptional profiling of GE cells
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“a second group of branches (i.e. precursor state 2) expressed known projection neuron marker genes (i.e. Isl1, Ebf1; Fig. 3E; Supplementary Table 4)”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Transcriptional profiling of GE cells
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“we performed a differential expression analysis and found a small number of transcription factors enriched in mitotic progenitors within particular eminences”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Transcriptional profiling of GE cells
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“As expected, neurons born at these sequential timepoints were distributed progressively along the MT timeline (Fig. 1H, Extended Data Fig. 1).”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Transcriptional profiling of GE cells
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“we found that, as expected20, more than 80% of Dlx6a-Cre fate mapped cortical cells at E18.5 mapped to precursor state 1, based on their expression of canonical regulators of interneuron development”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Diversity emerges from a common precursor state
What the sources say
- Not checked yetcites [20] Wichterle, H ., Turnbull, D. H ., Nery, S ., Fishell, G. & Alvarez-Buylla, A. In utero fate mapping reveals distinct migratory pathways and fates of neurons born in the mammalian basal forebrain. Development 128, 3759–3771 (2001) source
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“even though branched trajectories for each eminence were calculated independently, branch gene expression markers were highly correlated across eminences”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Transcriptional profiling of GE cells
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“The remaining Dlx6a-Cre fate mapped cortical population mapped to precursor states 2 and 3 (Fig. 3I, Extended Data Fig. 5), likely including the Meis2-expressing CGE-derived GABAergic population that has been recently described21”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Diversity emerges from a common precursor state
What the sources say
- Not checked yetcites [21] Frazer, S . et al. Transcriptomic and anatomic parcellation of 5-HT3AR expressing cortical interneuron subtypes revealed by single-cell RNA sequencing. Nat. Commun. 8, 14219 (2017) source
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“Embryonic stages also displayed strong evidence of interneuron specification.”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Diversity emerges from a common precursor state
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“genes that our analysis identified as being differentially expressed between the eminences31”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
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“Each eminence was analyzed independently, revealing nearly identical patterns.”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
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In the paper
“heterogeneity was driven primarily by maturation state or cell cycle”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Transcriptional profiling of GE cells
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“Within this population, the expression of early, intermediate, and late marker genes was strongly associated with the top diffusion map coordinates (DMC; Extended Data Fig. 1).”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Transcriptional profiling of GE cells
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In the paper
“Surprisingly, the majority of dynamically expressed genes followed robust and highly reproducible sequential waves of gene expression in all three eminences”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Transcriptional profiling of GE cells
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In the paper
“we can see that the ‘cardinal type’ separation we observe via integrated analysis (Figure 4B-D) is consistent with an independent analysis of each dataset.”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
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“One group of highly correlated branches (i.e. precursor state 1) expressed known regulators of interneuron development (i.e. Arx, Maf; Fig. 3E; Supplementary Table 4)”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Transcriptional profiling of GE cells
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“Diffusion map analysis of eminence datasets suggests a pan-eminence developmental continuum.”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
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In the paper
“The remaining 96.7% of cells were GE-derived neuronal progenitors and precursors (e.g., Dlx1; Fig. 1B, C).”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Transcriptional profiling of GE cells
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In the paper
“Notably, segregation into subtypes became evident at different developmental stages.”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Diversity emerges from a common precursor state
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“The minority of Dlx6a-positive cortical cells mapping to precursor states 2 and 3 primarily co-express Gad1 and Meis2”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
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In the paper
“cells from different branches could largely be separated into ‘early’, ‘intermediate’, and ‘late’ regions of mitotic pseudotime”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
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In the paper
“with one branch being largely defined by the expression of pro-neural cell cycle regulators (e.g. Ascl1).”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
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“C) Single cell heatmaps showing the best transcriptomic markers marking each subtype, for the Sst, Vip, and Id2 cardinal types, within P10 cells. We did not observe any statistically significant markers subdividing Pvalb subtypes.”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
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In the paper
“Sequencing MGE progenitors at significantly higher depth with plate-based scRNA-seq revealed no transcriptomic evidence of similar bifurcations within mitotic cells”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Transcriptional profiling of GE cells
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“Rare mitotic cells expressing canonical branch markers do not segregate on the diffusion plot.”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
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“Comparing the expression profiles of cortical interneuron precursors (precursor state 1) from the MGE and CGE revealed differentially expressed genes whose expression patterns are largely maintained in the cortex at later timepoints”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Diversity emerges from a common precursor state
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In the paper
“Consistent with our earlier findings (Fig. 2), we did not observe common sources of variation shared between adult interneurons and mitotic progenitors.”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Diversity emerges from a common precursor state
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“identifies rare contaminating populations of microglia (micro), astrocytes (Astro), oligodendrocyte precursor cells (OPCs) and oligodendrocytes (Oligo); smooth muscle cells (SMC), stem cells (SC).”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
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In the paper
“Dlx6a-Cre;RCEloxP positive E18.5 cells from the subcortex primarily map to branch 2 and 3”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
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In the paper
“utilizing a publicly available dataset22,23, we identified 14 inhibitory interneuron subpopulations that encompass known anatomically and physiologically defined subtypes24,25”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Diversity emerges from a common precursor state
What the sources say
- Not checked yetcites [22] Tasic, B . et al. Adult mouse cortical cell taxonomy revealed by single cell transcriptomics. Nat. Neurosci. 19, 335–346 (2016) source
- Not checked yetcites [23] Tremblay, R ., Lee, S. & Rudy, B. GABAergic interneurons in the neocortex: from cellular properties to circuits. Neuron 91, 260–292 (2016) source
- Not checked yetcites [24] Petilla Interneuron Nomenclature Group. Petilla terminology: nomenclature of features of GABAergic interneurons of the cerebral cortex. Nat. Rev. Neurosci. 9, 557–568 (2008) source
- Not checked yetcites [25] Butler, A. & Satija, R. Integrated analysis of single cell transcriptomic data across conditions, technologies, and species. Preprint at https://www.biorxiv.org/content/early/2017/07/18/164889 (2017) source
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“we found that a subset of embryonic cardinal type markers from our mouse dataset (including Mef2c) was also differentially expressed in adult human interneurons”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Diversity emerges from a common precursor state
What the sources say
- Not checked yetcites [30] Monory, K . et al. The endocannabinoid system controls key epileptogenic circuits in the hippocampus. Neuron 51, 455–466 (2006) source
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In the paper
“These could be allocated into non-overlapping cardinal types of cortical interneurons (Pvalb, Sst, Vip, Id2, Th, Nos1, Igfbp6).”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Diversity emerges from a common precursor state
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In the paper
“A subset of embryonic markers of cardinal type specification in mouse are conserved in adult human neurons”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
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In the paper
“Mef2c cKO results in a reduction in Pvalb density in all cortical layers except for layer 1”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
plaindirectn = 4 ·- Asserted: passes — The authors put it forward as true.
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In the paper
“F) Single cell heatmaps showing the best transcriptomic markers marking each subtype, for the Sst, Vip, and Id2 cardinal types, within E18.5 cells. We did not observe any statistically significant markers subdividing Pvalb subtypes.”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“Diversity is first apparent in the regional expression of a limited number of transcription factors within the ganglionic eminences (GEs)2,3.”
§ Developmental diversification of cortical inhibitory interneurons > Introduction
What the sources say
- Not checked yetcites [2] Flames, N . et al. Delineation of multiple subpallial progenitor domains by the combinatorial expression of transcriptional codes. J. Neurosci. 27, 9682–9695 (2007) source
- Not checked yetcites [3] Yun, K ., Garel, S ., Fischman, S. & Rubenstein, J. L. R. Patterning of the lateral ganglionic eminence by the Gsh1 and Gsh2 homeobox genes regulates striatal and olfactory bulb histogenesis and the growth of axons through the basal ganglia. J. Comp. Neurol. 461, 151–165 (2003) source
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“Our analysis revealed that the ASD-associated transcription factor Mef2c delineates early Pvalb-precursors, and is essential for their development.”
- Also stated in: § Diversity emerges from a common precursor state · hedged
“indicating that Mef2c is essential for the generation of this population.”
§ Developmental diversification of cortical inhibitory interneurons > Abstract
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In the paper
“It seems probable that the superimposition of precursor state genes and eminence-specific genes coordinately act to bestow both the common and unique characteristics within particular GABAergic populations, respectively.”
§ Developmental diversification of cortical inhibitory interneurons > DISCUSSION
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In the paper
“Thus, precursor genes likely direct the developmental cascade and acquisition of general properties that are shared within a given type.”
§ Developmental diversification of cortical inhibitory interneurons > DISCUSSION
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“Monocle2 pseudotime was strongly correlated with our maturation trajectory (both pearson and spearman R=0.94).”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
What the sources say
- Not checked yetcites [13] Qiu, X . et al. Reversed graph embedding resolves complex single-cell trajectories. Nat. Methods 14, 979–982 (2017) source
boostedcorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“likely representing a CGE-derived GABAergic population.”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
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
“as a validation of the original Drop-seq datasets that were performed on WT mice.”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
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
“Using PCA to reconstruct developmental maturation returns nearly identical results to the diffusion map analysis in Fig. 1.”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
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
“consistent with our interpretation of these branches as precursor states for projection neurons”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
hedgeddirect- Asserted: passes — The authors put it forward as true.
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- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
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
“Importantly, the results of our integrated analyses were in agreement with independent unsupervised analysis of each developmental stage (Extended Fig. 8).”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Diversity emerges from a common precursor state
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
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 distinct differentiation modules are reflective of the four major cardinal types of cortical interneuron precursors.”
§ Developmental diversification of cortical inhibitory interneurons > DISCUSSION
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: unclear — It is unclear why the paper says it holds.
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
“our list of cardinal type and subtype markers that are conserved from the ganglionic eminences through adulthood suggests a set of genetic regulators that may play important roles in this process.”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Diversity emerges from a common precursor state
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
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
“Hence, although each GE generates different cell populations, upon becoming postmitotic, cells from all eminences pass through conserved precursor states.”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Transcriptional profiling of GE cells
plain- Asserted: passes — The authors put it forward as true.
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- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
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
“Therefore, the genes we identified as defining embryonic cardinal types are candidates for regulating interneuron fate determination and maintenance across species.”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Diversity emerges from a common precursor state
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
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
“Postmitotic cells in the ganglionic eminences branch into distinct precursor states, representing populations fated to give rise to interneurons or projection neurons.”
§ Developmental diversification of cortical inhibitory interneurons > DISCUSSION
plaindirect- Asserted: passes — The authors put it forward as true.
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- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
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
“our findings indicate that components of the transcriptional networks underlying interneuron fate specification are conserved between mouse and human, including Mef2c and other genes associated with neuropsychiatric disorders.”
§ Developmental diversification of cortical inhibitory interneurons > DISCUSSION
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“We obtained very similar trajectories using approaches based on PCA or reverse graph embedding (Extended Data Fig. 1)13”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Transcriptional profiling of GE cells
What the sources say
- Not checked yetcites [13] Qiu, X . et al. Reversed graph embedding resolves complex single-cell trajectories. Nat. Methods 14, 979–982 (2017) source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
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
“Therefore, these cells are correctly mapped as ‘unassigned’.”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- It may state two separate claims as one. 33
- Probably not a substantial claim. 9
The cited sources that could be checked couldn’t confirm or dispute this claim.
In the paper
“The trend overall shows that genes with peak expression at low MS tend to have higher expression in the VZ, and as MS rank increases the expression pattern shifts to the subventricular zone (SVZ) and then to the MZ”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
What the sources say
- Could not verifycites [31] Madisen, L. et al. A robust and high-throughput Cre reporting and characterization system for the whole mouse brain. Nat. Neurosci. 13, 133–140 (2010) sourceExperimental — accuracy not yet measured
The Results sections on Cre recombination patterns and fluorescent labeling discuss reporter-gene expression in mouse brain regions, not gene expression ranked by maturation score. Searches for maturation score and the ventricular, subventricular, and mantle zones found no passage addressing the claimed VZ-to-SVZ-to-MZ shift. (LLM, conf=0.75)
plaincorrelational- Asserted: passes — The authors put it forward as true.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Could not verify
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“By integrating datasets across developmental timepoints, we identified shared sources of transcriptomic heterogeneity between adult interneurons and their precursors, revealing the embryonic emergence of interneuron cardinal subtypes.”
§ Developmental diversification of cortical inhibitory interneurons > Abstract
plaincorrelational- Asserted: passes — The authors put it forward as true.
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- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — 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 number of conserved DE genes grow over time. Same analysis for Pvalb vs. Sst subsets (Middle), and Vip vs. Id2 subsets (Right).”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Developmental progression and cell cycle were the primary sources of transcriptional variance in these progenitors (Supplementary Methods), with maturation proportionally explaining six-fold more variance compared to eminence-of-origin”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Transcriptional profiling of GE cells
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Genetic fate mapping using Lhx8-Cre/cerulean demonstrates that MGE branch three precursors give rise to the entire breadth of cholinergic projection (Globus Pallidus and Nucleus Basalis) and interneuron (striatum) populations.”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
boosteddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Mitotic cells fall within a homogeneous point cloud, with low variance on PC1 and PC2, showing no evidence of fate bifurcation.”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — 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 vast majority of Dlx6a-Cre;RCEloxP positive E18.5 cortical cells map to the interneuron precursor state, and are split between MGE and CGE-derived precursors.”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — 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 cumulative longitudinal use of a constitutive Cre driver also results in extensive labeling of cortical interneurons due to transient expression within this population.”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“By E18, all cardinal types of interneurons could be identified, and additional subtypes appeared to be transcriptionally specified as well”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Diversity emerges from a common precursor state
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In-situ hybridization (ISH) confirmed that these waves describe the sequential expression of stem-cell (e.g. Nes), proneural (e.g., Ascl1), and neurogenic genes (e.g. Dcx; Fig. 2C), roughly correlating with the spatiotemporal progression from the VZ to the mantle zone (MZ)”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Transcriptional profiling of GE cells
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Of all cells, 3,432 GABAergic interneurons were easily identified by the expression of Gad1 and depletion of Slc17a7, and were selected for downstream analysis.”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
A result the paper reports from its own data — 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 third group of branches (i.e. precursor state 3) exhibited weaker correlation across eminences, with the transcription factor Lhx8 representing a marker gene for the MGE Branch 3”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Transcriptional profiling of GE cells
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Integrated analysis with the P56 dataset results in clearer separation, and enables us to map developmental precursors to adult subtypes.”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
boosteddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Based on this alignment, P10 cells exhibited strong evidence of transcriptomic separation beyond cardinal types, (Fig. 4B), including clear segregation between Sst Martinotti versus non-Martinotti (X94), Vip bipolar versus multipolar, and Id2 neurogliaform versus non-neurogliaform interneuron subtypes”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Diversity emerges from a common precursor state
boostedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We first observed evidence of clear fate bifurcations as cells become postmitotic, and precursors from all GEs branched into distinct precursor states”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Transcriptional profiling of GE cells
boostedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“we identified rare populations that did not express canonical interneuron (IN) markers, likely representing false positives from FACS.”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“tSNE visualization and graph-based clustering of the 3,432 GABAergic cells reveals 14 clusters, which could be broadly grouped into cardinal types based on the expression of canonical markers”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“While we did observe computational evidence of branching, this does not represent fate bifurcations as we observed in postmitotic cells.”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“we observed a separation of Pvalb- and Sst-precursor cells within the E13.5 postmitotic populations (Fig. 4D), and identified transcriptomic markers that were conserved into adulthood”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Diversity emerges from a common precursor state
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“branching trajectories represented the most significant source of variation in these cells, with an increasing contribution attributable to eminence of origin compared to mitotic progenitors”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Diversity emerges from a common precursor state
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“A minority of E13.5 cells also mapped to Vip and Id2 subsets, but conserved transcriptomic markers did not pass statistical significance until E18.5”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Diversity emerges from a common precursor state
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Genetic ‘fate-mapping’ using Lhx8-Cre suggested that these neurons account for the majority, if not all of the cholinergic projection and interneuron populations within the nucleus basalis, medial septum, and striatum, respectively, as well as the majority of Pvalb-positive projection neurons in the globus pallidus5,6”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Transcriptional profiling of GE cells
What the sources say
- Not checked yetcites [5] Nóbrega-Pereira, S . et al. Origin and molecular specification of globus pallidus neurons. J. Neurosci. 30, 2824–2834 (2010) source
- Not checked yetcites [6] Zhao, Y . et al. The LIM-homeobox gene Lhx8 is required for the development of many cholinergic neurons in the mouse forebrain. Proc. Natl Acad. Sci. USA 100, 9005–9010 (2003) source
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — 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 components reflect our previously defined maturation trajectory, with DMC1 separating mitotic cells (left).”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Our Lhx6-GFP-negative dataset contains both mitotic and postmitotic cells from the CGE and diffusion map analysis shows our previously defined maturation trajectory.”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“the clear emergence of Sst, Vip and Id2 subtypes was apparent for a subset of cells at E18.5 (Extended Data Figure 8), but we were unable to clearly subdivide Pvalb neurons by P10, in accordance with their late maturation28.”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Diversity emerges from a common precursor state
What the sources say
- Not checked yetcites [28] Harrington, A. J . et al. MEF2C regulates cortical inhibitory and excitatory synapses and behaviors relevant to neurodevelopmental disorders. eLife 5, 140 (2016) source
boosted- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Diffusion map analysis of these cells returned only two significant principal components, with no evidence of further structure.”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“observed that MT recapitulated known dynamics associated with neuronal maturation (Fig. 1E) while also segregating GE cells into ‘mitotic’ and ‘postmitotic’ phases”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Transcriptional profiling of GE cells
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“This diverse group of neurons is developmentally derived from progenitors residing in embryonic proliferative zones known as the medial, caudal and lateral ganglionic eminences (MGE, CGE, LGE, respectively)1.”
§ Developmental diversification of cortical inhibitory interneurons > Introduction
What the sources say
- Not checked yetcites [1] Kepecs, A. & Fishell, G. Interneuron cell types are fit to function. Nature 505, 318–326 (2014) source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“The MGE and CGE are known to produce non-overlapping types of cortical interneurons16.”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Transcriptional profiling of GE cells
What the sources say
- Not checked yetcites [16] Rudy, B ., Fishell, G ., Lee, S. & Hjerling-Leffler, J. Three groups of interneurons account for nearly 100% of neocortical GABAergic neurons. Dev. Neurobiol. 71, 45–61 (2011) source
boosted- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably 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
“Supplementing these more general programs are the eminence-specific genes that, for example, may direct the axons of parvalbumin cortical interneurons to form perisomal baskets and the efferents of somatostatin cortical interneurons to reliably target dendrites.”
§ Developmental diversification of cortical inhibitory interneurons > DISCUSSION
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds. It may state two separate claims as one.
In the paper
“Cells expressing both genes are likely projection neuron precursors that have recently been described in the CGE21, but whose progeny is not captured in the mouse visual cortex dataset.”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
What the sources say
- Not checked yetcites [21] Frazer, S . et al. Transcriptomic and anatomic parcellation of 5-HT3AR expressing cortical interneuron subtypes revealed by single-cell RNA sequencing. Nat. Commun. 8, 14219 (2017) source
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
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 avoid the possibility of FACS false negative MGE cells contaminating our Lhx6-GFP-negative dataset, we clustered the postmitotic cells from this dataset, and filtered out three rare clusters where Lhx6 mRNA expression was detected in more than 20% of cells”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“We manually dissected the embryonic day (E)13.5 MGE or E14.5 CGE and LGE from wild type mouse embryos, timepoints corresponding to peak neurogenesis in these structures7,8”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Transcriptional profiling of GE cells
What the sources say
- Not checked yetcites [7] Inan, M ., Welagen, J. & Anderson, S. A. Spatial and temporal bias in the mitotic origins of somatostatin- and parvalbumin-expressing interneuron subgroups and the chandelier subtype in the medial ganglionic eminence. Cereb. Cortex 22, 820–827 (2012) source
- Not checked yetcites [8] Miyoshi, G . et al. Genetic fate mapping reveals that the caudal ganglionic eminence produces a large and diverse population of superficial cortical interneurons. J. Neurosci. 30, 1582–1594 (2010) source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably 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
“Thus, our data reveal how postmitotic pan-eminence transcriptional programs (precursor states) emerge, and in parallel, eminence-specific transcriptional programs escalate.”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Diversity emerges from a common precursor state
boostedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“Genome-wide association studies have linked mutations in this gene to Alzheimer’s, schizophrenia, and other neurodevelopmental disorders29.”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Diversity emerges from a common precursor state
What the sources say
- Not checked yetcites [29] Habib, N . et al. Massively parallel single-nucleus RNA-seq with DroNc-seq. Nat. Methods 14, 955–958 (2017) source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“These cells have been recently described as being present in the cortical white matter and likely represent projection neuron precursors21.”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
What the sources say
- Not checked yetcites [21] Frazer, S . et al. Transcriptomic and anatomic parcellation of 5-HT3AR expressing cortical interneuron subtypes revealed by single-cell RNA sequencing. Nat. Commun. 8, 14219 (2017) source
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“We performed latent variable regression to mitigate heterogeneity resulting from cell-cycle state10,11 (Extended Data Fig. 1), preventing subsequent analysis from being dominated by mitotic phase-specific gene expression”
§ Developmental diversification of cortical inhibitory interneurons > RESULTS > Transcriptional profiling of GE cells
What the sources say
- Not checked yetcites [10] Buettner, F . et al. Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells. Nat. Biotechnol. 33, 155–160 (2015) source
- Not checked yetcites [11] Tirosh, I . et al. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science 352, 189–196 (2016) source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
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
“Therefore, our FlashTag maturation trajectory serves as complementary validation of our Drop-seq maturation trajectory, and exhibits strong association with biological time.”
§ Developmental diversification of cortical inhibitory interneurons > Extended Data
boostedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper relies on this without support.
The genetic programs that drive interneuron fate specification and maintenance are not well understood.
“the genetic programs driving interneuron fate specification and maintenance are not well understood”
The paper relies on this without support.
It remains unclear how early sources of heterogeneity generate the vast diversity of adult interneurons.
“it remains unclear how these early sources of heterogeneity generate the vast diversity of adult interneurons”
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 source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“The cardinal identity of a cell is probably already instilled at the postmitotic stage during development9,61,62,63,64, and its subsequent phenotypic differentiation and expression are regulated by extrinsic signals such as cell interactions and neural activity.”
From The diversity of GABAergic neurons and neural communication elements (2019) · cites this paper as [61]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Lhx6–a transcription factor–participates in cell fate determination of MGE types, whereas Lamp5+ neocortical interneurons come from the CGE35.”
From Innovations present in the primate interneuron repertoire (2020) · cites this paper as [35]
Experimental — accuracy not yet measuredIn the citing paper
“a contemporaneous study based on a different scRNA-seq approach found no evidence for early embryonic specification of interneurons into specific cell types”
From Development and Functional Diversification of Cortical Interneurons (2018) · cites this paper as Mayer et al., 2018
In the citing paper
“Cortical excitatory neuron transcriptomes may be more heterogeneous due to their developmental origin spread across the dorsal telencephalon, compared with GABAergic populations that originate in the ganglionic eminences and migrate to cortex (Mayer et al., 2018).”
From Single-Cell Sequencing of Brain Cell Transcriptomes and Epigenomes (2021) · cites this paper as Mayer et al., 2018
In the citing paper
“scRNA-seq reveals how neuronal and glial cell type identities emerge in developing mouse (Mayer et al., 2018; Telley et al., 2019; Tiklová et al., 2019) and human brain (Li et al., 2018; Nowakowski et al., 2017; Pollen et al., 2015), and even across whole organisms (Farrell et al., 2018).”
From Single-Cell Sequencing of Brain Cell Transcriptomes and Epigenomes (2021) · cites this paper as Mayer et al., 2018
In the citing paper
“(and both are expressed in the cortical Lamp5+ Lhx6+ type)”
From Innovations present in the primate interneuron repertoire (2020) · cites this paper as [35]
In the citing paper
“In mouse mature cortical interneurons, Id2 and Lamp5 are expressed in nearly identical populations35”
From Innovations present in the primate interneuron repertoire (2020) · cites this paper as [35]
In the citing paper
“Developmentally, Sst+and Pavlb+ originate from the medial ganglionic eminence (MGE), while the Vip+ originate from the caudal ganglionic eminence (CGE)15.”
From Cell type-specific transcriptional programs in mouse prefrontal cortex during adolescence and addiction (2019) · cites this paper as [15]
In the citing paper
“and are likely the remaining non-MGE origin cells (arising from CGE and/or POA)14–16”
From Cell type-specific transcriptional programs in mouse prefrontal cortex during adolescence and addiction (2019) · cites this paper as [15]
In the citing paper
“For example, Mayer et al (2018) fit a negative binomial model to count data, using technical covariates such as the read depth and the number of counts per gene to fit the model parameters.”
From Current best practices in single-cell RNA-seq analysis: a tutorial (2019) · cites this paper as Mayer et al, 2018
Citations
Cites
WGCNA: an R package for weighted correlation network analysis
Langfelder, P., & Horvath, S. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-559 · Cited by 27,252
Fast unfolding of communities in large networks
Blondel, V. D., Guillaume, J.-L., Lambiotte, R., & Lefebvre, E. (2008) · Journal of Statistical Mechanics: Theory and Experiment · doi:10.1088/1742-5468/2008/10/p10008 · Cited by 21,424
Integrated analysis of single cell transcriptomic data across conditions, technologies, and species
Butler, A., & Satija, R. (2017) · doi:10.1101/164889 · Cited by 13,200
Self-citationIntegrating single-cell transcriptomic data across different conditions, technologies, and species
Butler, A., Hoffman, P., Smibert, P., Papalexi, E., & Satija, R. (2018) · Nature Biotechnology · doi:10.1038/nbt.4096 · Cited by 13,174
Self-citationTrapnell, C., Cacchiarelli, D., Grimsby, J., Pokharel, P., Li, S., Morse, M., Lennon, N. J., Livak, K. J., Mikkelsen, T. S., & Rinn, J. L. (2014) · Nature Biotechnology · doi:10.1038/nbt.2859 · Cited by 7,314
Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets.
Macosko, E. Z., Basu, A., Satija, R., Nemesh, J., Shekhar, K., Goldman, M., Tirosh, I., Bialas, A. R., Kamitaki, N., Martersteck, E. M., et al. (2015) · Cell · doi:10.1016/j.cell.2015.05.002 · Cited by 7,110
Self-citationA robust and high-throughput Cre reporting and characterization system for the whole mouse brain
Madisen, L., Zwingman, T. A., Sunkin, S. M., Oh, S. W., Zariwala, H. A., Gu, H., Ng, L. L., Palmiter, R. D., Hawrylycz, M. J., Jones, A. R., et al. (2010) · Nature Neuroscience · doi:10.1038/nn.2467 · Cited by 6,907
Genome-wide atlas of gene expression in the adult mouse brain
Lein, E. S., Hawrylycz, M. J., Ao, N., Ayres, M., Bensinger, A., Bernard, A., Boe, A. F., Boguski, M. S., Brockway, K. S., Byrnes, E. J., et al. (2007) · Nature · doi:10.1038/nature05453 · Cited by 5,572
Reversed graph embedding resolves complex single-cell trajectories
Qiu, X., Mao, Q., Tang, Y., Wang, L., Chawla, R., Pliner, H. A., & Trapnell, C. (2017) · Nature Methods · doi:10.1038/nmeth.4402 · Cited by 5,070
Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq
Tirosh, I., Izar, B., Prakadan, S. M., Wadsworth, M. H., Treacy, D., Trombetta, J. J., Rotem, A., Rodman, C., Lian, C., Murphy, G., et al. (2016) · Science · doi:10.1126/science.aad0501 · Cited by 4,944
Cited by
Sorted by citations
Comprehensive Integration of Single-Cell Data
Stuart, T., Butler, A., Hoffman, P., Hafemeister, C., Papalexi, E., Mauck, W. M., Hao, Y., Stoeckius, M., Smibert, P., & Satija, R. (2019) · Cell · doi:10.1016/j.cell.2019.05.031 · Cited by 15,453
Self-citationIntegrating single-cell transcriptomic data across different conditions, technologies, and species
Butler, A., Hoffman, P., Smibert, P., Papalexi, E., & Satija, R. (2018) · Nature Biotechnology · doi:10.1038/nbt.4096 · Cited by 13,174
Self-citationThe single-cell transcriptional landscape of mammalian organogenesis
Cao, J., Spielmann, M., Qiu, X., Huang, X., Ibrahim, D. M., Hill, A. J., Zhang, F., Mundlos, S., Christiansen, L., Steemers, F. J., et al. (2019) · Nature · doi:10.1038/s41586-019-0969-x · Cited by 4,490
“For example, scRNA-seq recently revealed remarkable heterogeneity in neurons and myocardiocytes during mouse development 8,9 .”
Current best practices in single-cell RNA-seq analysis: a tutorial
Luecken, M. D., & Theis, F. J. (2019) · Molecular Systems Biology · doi:10.15252/msb.20188746 · Cited by 2,231
“Popular platforms such as Seurat (Butler et al , 2018), Scater (McCarthy et al , 2017), or Scanpy (Wolf et al , 2018) provide integrated environments to develop pipelines and contain large analysis toolboxes.”
MethodInfluentialThe bone marrow microenvironment at single-cell resolution
Tikhonova, A. N., Dolgalev, I., Hu, H., Sivaraj, K. K., Hoxha, E., Cuesta-Domínguez, Á., Pinho, S., Akhmetzyanova, I., Gao, J., Witkowski, M., et al. (2019) · Nature · doi:10.1038/s41586-019-1104-8 · Cited by 936
Self-citation
Metadata
- Authors
- Mayer, C., Hafemeister, C., Bandler, R. C., Machold, R., Batista Brito, R., Jaglin, X., Allaway, K., Butler, A., Fishell, G., & Satija, R.
- Affiliations
- Broad Institute (US)
- New York Genome Center (US)
- NYU Langone Health (US)
- Harvard University (US)
- Corresponding author
- Fishell, Gord
- Satija, Rahul
- ORCID
- Venue
- Nature
- Published
- 2018-03-05
- Volume
- 555
- Issue
- 7697
- Pages
- 457-462
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC6052457
- OpenAlex
- W2791731597
- Semantic Scholar
- 7450ce01a65bcf74dd0dabd3df9b6cf350b4401b
- Cited by
- 492
- References
- 42
- Citations by year
- 2026: 39 · 2025: 43 · 2024: 50 · 2023: 53 · 2022: 65 · 2021: 76 · 2020: 73 · 2019: 59 · 2018: 34
- FWCI
- 22.24
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- Nature (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- National Science Foundation (1342536)
- Simons Foundation (P01 NS074972)
- Deutsche Forschungsgemeinschaft
- National Institutes of Health (NIH DP2, 1dp2hg009623-01, MH071679, NS074972)
- National Institute of Mental Health (F30MH114462, R01MH111529, R01MH071679, R37MH071679)
- National Human Genome Research Institute (DP2-HG-009623)
- National Institute of General Medical Sciences (T32GM007308)
- National Institute of Neurological Disorders and Stroke (P01NS074972, F31NS103398, R01NS039007, R01NS081297)
- Topics
- Life Sciences › Neuroscience › Developmental Neuroscience › Neurogenesis and neuroplasticity mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Keywords
- cortical interneurons, MEF2C, parvalbumin neurons, ganglionic eminence, transcriptional heterogeneity, interneuron subtypes, developmental trajectories, transcription factors, neuropsychiatric disorders, mouse embryo
- MeSH terms
- Animals, Cell Differentiation, Embryo, Mammalian, Female, Ganglia, Humans, Interneurons, Male, Mitosis, Neural Inhibition, Parvalbumins, Visual Cortex, RNA, Small Cytoplasmic, Gene Expression Profiling, Mice, Single-Cell Analysis, MEF2 Transcription Factors
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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.
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