The DOI matches its Crossref record; 78 of the 78 references it cites were found in a registry or an index; 1 of the 53 sources its claims cite were checked for support.
Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type
Open accessPublished version of a preprint
Abstract
We describe convergent evidence from transcriptomics, morphology, and physiology for a specialized GABAergic neuron subtype in human cortex. Using unbiased single-nucleus RNA sequencing, we identify ten GABAergic interneuron subtypes with combinatorial gene signatures in human cortical layer 1 and characterize a group of human interneurons with anatomical features never described in rodents, having large ‘rosehip’-like axonal boutons and compact arborization. These rosehip cells show an immunohistochemical profile (GAD1+CCK+, CNR1–SST–CALB2–PVALB–) matching a single transcriptomically defined cell type whose specific molecular marker signature is not seen in mouse cortex. Rosehip cells in layer 1 make homotypic gap junctions, predominantly target apical dendritic shafts of layer 3 pyramidal neurons, and inhibit backpropagating pyramidal action potentials in microdomains of the dendritic tuft. These cells are therefore positioned for potent local control of distal dendritic computation in cortical pyramidal neurons. The authors use single-nucleus RNA-seq to identify 10 GABAergic interneuron subtypes in human cortex layer 1. Molecular, morphological, and physiological evidence points to an emerging human cell type, the rosehip cell, not found in other species.
Overview
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
84 Own result · 24 Not checked yet · 23 Own method · 17 Own interpretation · 5 No basis given · 1 Supported so far
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
“Rosehip cells in layer 1 make homotypic gap junctions”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Abstract
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.
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
“Somata and dendrites of RCs were confined to layer 1 with only distal dendrites occasionally penetrating layer 2.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Rosehip cells: novel morphological features in layer 1 of the human cerebral cortex
plainn = 10- 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 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
“predominantly target apical dendritic shafts of layer 3 pyramidal neurons”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Abstract
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.
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
“Proximal dendrites and somata of RCs were decorated with stub-like spines.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Rosehip cells: novel morphological features in layer 1 of the human cerebral cortex
plainn = 10- 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 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
“Unbiased recordings of layer 1 cell types yielded a set of interneurons with complete axo-somato-dendritic recovery (n=76).”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Rosehip cells: novel morphological features in layer 1 of the human cerebral cortex
plainn = 76- 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 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 layer 1 MTG transcriptomic clusters expressed either SST (i1,i2), VIP (i6, i9, i10), or neither marker”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results
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.
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
“inhibit backpropagating pyramidal action potentials in microdomains of the dendritic tuft”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Abstract
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.
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
“whose specific molecular marker signature is not seen in mouse cortex”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Abstract
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.
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
“Using unbiased single nucleus RNA sequencing, we identify ten GABAergic interneuron subtypes with combinatorial gene signatures in human cortical layer 1”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Abstract
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.
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
“Furthermore, each cluster showed highly selective expression of known and previously uncharacterized individual marker genes.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results
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. 59
- Probably not a substantial claim. 32
- The quote only partly states this claim. 1
The sources with a verdict support this claim; the rest weren’t checked yet, have no full text we could read, or their verdicts aren’t rated yet.
In the paper
“Thus, RCs may provide supplementary inhibitory control required to balance the potentially higher excitability in human dendrites8 and modulate interactions between long range excitatory connections arriving to layer 1 and backpropagating action potentials suggested to participate in interhemispheric modulation45.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Discussion
What the sources say
- Supportedcites [8] Eyal, G. et al. Unique membrane properties and enhanced signal processing in human neocortical neurons. eLife 5, e16553 (2016). source
Split into 2 atoms — 2 confirmed, 0 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
- Not checked yetcites [45] Palmer, L. M. et al. The cellular basis of GABA(B)-mediated interhemispheric inhibition. Science 335, 989–993 (2012). source
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.
It may state two separate claims as one.
- Supported
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Therefore, there appear to be ten inhibitory cell types within layer 1, although it is not clear whether any of these types are completely restricted to layer 1.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results
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.
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
“voltage-gated ion channels and GABA and glutamate receptor subunits show diverse expression patterns among interneurons, including highly cell type-specific expression of CACNA2D1, GABRG1, KCNH5, and SCN5A”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results
boostedcorrelational- 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
“Light microscopic examination of these cells identified neurons with previously described morphological features, e.g. neurogliaform cells (NGFCs, n=16, 21%; Fig.2C,D)1,21,24 as well as a novel group of interneurons having large, rosehip-shaped axonal boutons forming very compact, bushy arborizations (rosehip cells, RCs, n=10, 13%; Fig.2A,D).”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Rosehip cells: novel morphological features in layer 1 of the human cerebral cortex
plainn = 76- 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 bouton density of rosehip, neurogliaform and BCs almost monotonously decreased with increasing distances from the soma; however, bouton densities were lower in BCs 30-50 µm (p<0.04 for 30-50, MW U-test) and higher in NGFCs 70-220 µm (p<0.02, MW U-test) and in BCs 130-220 µm (p<0.03) from the soma.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Rosehip cells: novel morphological features in layer 1 of the human cerebral cortex
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
“Total dendritic length (1.96±0.90 mm) and dendritic node frequency per 100 µm (0.66±0.21) of RCs were significantly different from those of BCs (3.41±0.58 mm, p<0.031; 0.29±0.10, p<0.009, respectively, MW U-test) and were similar to those of NGFCs (2.62±1.08 mm, 1.50±1.47).”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Rosehip cells: novel morphological features in layer 1 of the human cerebral cortex
plainn = 6 ·- 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
“Maximal radial extent of axon of RCs (263.42±69.09 µm) was significantly smaller than that of BCs (713.22±124.87 µm, p<0.005, MW U-test), but were not different from those of NGFCs (323.18±49.60 µm).”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Rosehip cells: novel morphological features in layer 1 of the human cerebral cortex
plainn = 5 ·- 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 number of primary dendrites of RCs (5.50±1.87) was similar to that of BCs (6.2±2.17, n=5) and was significantly fewer compared to NGFCs (8.6±2.19, n=5, p<0.04, Mann-Whitney (MW) U-test).”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Rosehip cells: novel morphological features in layer 1 of the human cerebral cortex
plainn = 5 ·- 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 rosehip cells show an immunohistochemical profile (GAD1/CCK-positive, CNR1/SST/CALB2/PVALB-negative) matching a single transcriptomically-defined cell type”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Abstract
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
“RCs had longer interbouton intervals compared to NGFCs (3.97±0.49 and 3.10±0.32 µm, respectively, p<0.038, MW U-test) and shorter compared to BCs (5.63±0.51 µm, p<0.024) measured as linear distances between neighboring boutons.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Rosehip cells: novel morphological features in layer 1 of the human cerebral cortex
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
“Interestingly, both SST and VIP (but not PVALB) are seen in human MTG layer 1 by ISH”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results
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
“characterize a novel group of human interneurons with anatomical features never described in rodents having large, “rosehip”-like axonal boutons and compact arborization”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Abstract
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.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“several of these markers appear to be related to interaction with endothelia, including endothelin receptor type A (EDNRA) and epidermal growth factor (EGF).”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results
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.
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 axon of RCs usually emerged from the basal part of the soma and gave rise to very compact, dense axonal trees predominantly arborizing in layer 1 with tortuous collaterals having spindle-shaped boutons with diameters not seen in other types of human layer 1 interneurons in our sample.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Rosehip cells: novel morphological features in layer 1 of the human cerebral cortex
plainn = 10- 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
“cluster i2 represents a cell type restricted to layer 2 since it also expresses LHX6 which is not found in layer 1”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results
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
“clusters corresponded to all major classes of neural cell types that were expected to be captured”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results
plainn = 2- 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. The quote only partly states this 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
“Targeted recordings increased the number of RCs in our database (n=120)”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Rosehip cells: novel morphological features in layer 1 of the human cerebral cortex
plaindirectn = 120- 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
“Total length (11.13±1.99 mm) and maximal horizontal extent of axons (287.75±70.15 µm) of RCs were significantly smaller than those of NGFCs (24.74±8.90 mm, 648.68±202.60 µm, respectively; p<0.005 for both, MW U-test) and BCs (31.16±14.79 mm, p<0.009; 1102.76±296.99 µm, p<0.005, respectively, MW U-test).”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Rosehip cells: novel morphological features in layer 1 of the human cerebral cortex
plainn = 5 ·- 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
“RCs received local excitatory inputs from layer 2-3 pyramidal cells sporadically (n=8, CR 5%) with monosynaptic EPSP amplitudes of 3.357±1.458 mV and paired pulse ratios of 0.68±0.12.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Function of rosehip cells in local microcircuits
plaincorrelationaln = 8- 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 states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“The RC represents a type with highly distinctive transcriptomic signature, a highly distinctive morphological, physiological and connectional phenotype, and a strong correspondence between these properties.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Discussion
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
“This revealed that RCs were immunopositive for CCK (n=10) but negative for CB1 cannabinoid receptor (CNR1, n=11), SST (n=9) and calretinin (CALB2; n=2; Fig.3A).”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Rosehip cells: novel morphological features in layer 1 of the human cerebral cortex
plainn = 10- 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
“frequencies of maximal impedance (fmax) in RCs (4.17±1.1 Hz) were significantly higher than in NGFCs (1.98±1.04 Hz; p<0.045) but the difference was not significant compared to unclassified interneurons (2.47±1.47 Hz, p<0.142).”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Intrinsic electrophysiological properties of rosehip cells
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
“Fast components of IPSPs arriving to RCs evoked by different presynaptic interneurons had similar amplitudes (0.982±0.705, 0.915±0.594 and 1.504±1.308 mV, respectively) and showed paired pulse depression with paired pulse ratios of (0.42±0.48, 0.27±0.04 and 0.71±0.26, respectively).”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Function of rosehip cells in local microcircuits
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
“time constants of RCs (7.3±3.7 ms) were similar to neurogliaform (8.9±2.4 ms, p<0.001) and faster compared to other cells (11.1±12.5 ms, p<0.001).”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Intrinsic electrophysiological properties of rosehip cells
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
“application of the CB1 receptor antagonist AM251 was ineffective in modulating RC evoked IPSPs (n=4, Fig.5H), supporting our results of single cell digital PCR, IHC and ISH data (Fig.3).”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Function of rosehip cells in local microcircuits
plainn = 4- 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
“The targeted application of single nucleus sequencing reported here has demonstrated a significantly higher degree of GABAergic neuron complexity in just one layer of the human cerebral cortex (10 types) than what has previously been described in all of the cortex (8 types22).”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Discussion
What the sources say
- Not checked yetcites [22] Lake, B. B. et al. Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain. Science 352, 1586–1590 (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
“The rosehip cluster i5 had a weak (r=0.34) reciprocal best match to mouse cluster Smad3, although several other human clusters (i7, i1, i4, i3) matched Smad3 almost as well (r>0.3).”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Rosehip cells: novel morphological features in layer 1 of the human cerebral cortex
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
“RCs also formed homologous electrical synapses (n=5, CR 57%) between each other (Fig.5K) and established convergent heterologous electrical synapses (n=2, CR 11%) with an unclassified layer 1 interneuron.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Function of rosehip cells in local microcircuits
plaincorrelationaln = 5- 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
“Input resistances of RCs (139.6±54.1 MΩ) were similar to those of NGFCs (160.1±55.9 MΩ) and lower compared to other interneurons (216.3±84.4 MΩ, p<0.001, Wilcoxon-test)”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Intrinsic electrophysiological properties of rosehip cells
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
“As predicted by the transcriptome data, RCs were positive for CCK, CPLX3, SV2C and TRPC3, and low (CNR1) or absent (NDNF) for genes not expressed by cells in that cluster”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Rosehip cells: novel morphological features in layer 1 of the human cerebral cortex
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
“expression of LAMP5, SV2C, EYA4 and CPLX3 is seen by ISH in human layer 1 (Fig.3C); similarly, as predicted by transcriptomics three of these four genes are also expressed in mouse layer 1 whereas cells expressing Eya4 are extremely rare.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Rosehip cells: novel morphological features in layer 1 of the human cerebral cortex
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
“Rosehip inputs simultaneous with backpropagating pyramidal action potentials were effective in suppressing Ca2+ signals only at sites that were neighboring (8±5 µm) to the putative synapses between the two cells. No effect of RCs was detected at dendritic sites one step further in distance (21±14 µm, Fig.6D-F).”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Function of rosehip cells in local microcircuits
plaindirectn = 4 ·- 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 CCK+/CNR1-/LAMP5+, CCK+/PDGFRA+/SOX13+, and CCK+/TRPC3+/CPLX3+ cells, as well as cells where CCK was swapped with other positive rosehip markers”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Rosehip cells: novel morphological features in layer 1 of the human cerebral cortex
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
“Expression correlations were quite low (r < 0.5), and clusters could only be reliably grouped into broad classes of cell types.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Rosehip cells: novel morphological features in layer 1 of the human cerebral cortex
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.
None of the sources cited for this claim have been checked yet.
In the paper
“Backpropagation of action potentials to dendrites of human neurons has been shown in previous studies13,29 and we confirmed these results by detecting dendritic Ca2+ responses following somatically elicited burst firing (100 ms current injections, 4 spikes/burst) in layer 3 pyramidal cells.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Function of rosehip cells in local microcircuits
What the sources say
- Not checked yetcites [13] Verhoog, M. B. et al. Mechanisms underlying the rules for associative plasticity at adult human neocortical synapses. J. Neurosci. 33, 17197–17208 (2013). source
- Not checked yetcites [29] Kerekes, B. P. et al. Combined two-photon imaging, electrophysiological, and anatomical investigation of the human neocortex in vitro. Neurophotonics 1, 011013 (2014). source
boosteddirect- 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
“The remaining n=5 (11 %) dendrites had no spines and received asymmetric synapses on the shaft were likely to be formed by interneurons.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Function of rosehip cells in local microcircuits
hedgedcorrelationaln = 5- 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
“GABAergic cells evoking IPSPs on RCs included layer 1 NGFCs (n=10, CR 100 %), RCs (n=2, CR 17%) and unclassified interneurons (n=14, CR 40%); however, none of the tested interneurons (n=9) having somata in layer 2 (defined as <70 µm below the layer 1/2 border) were connected to RCs.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Function of rosehip cells in local microcircuits
plainn = 10- 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
“further ultrastructural analysis of postsynaptic dendrites (n=46) revealed dendritic spines and sparse innervation by symmetrical synapses on the shaft, suggesting that these dendrites belonged to pyramidal cells (n=41, 86%, Fig.5J).”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Function of rosehip cells in local microcircuits
hedgedcorrelationaln = 46- 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 triple positive cells for this combination were sparsely distributed across layer 1, although not restricted to this layer (Suppl. Fig.5D).”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Rosehip cells: novel morphological features in layer 1 of the human cerebral cortex
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
“PDGFRA+ cells represent ~15% of GAD1+ cells, therefore an upper bound.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Rosehip cells: novel morphological features in layer 1 of the human cerebral cortex
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
“Furthermore, RCs were immunopositive for gamma-aminobutyric acid (GABA; n=2), for chicken ovalbumin upstream promoter transcription factor II (NR2F2; n=2) and negative for parvalbumin (n=3), neuronal nitric oxide synthase (n=4), neuropeptide Y (n=2), calbindin (n=2), and choline acetyltransferase (n=3; Suppl. Fig.5A).”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Rosehip cells: novel morphological features in layer 1 of the human cerebral cortex
plainn = 2- 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
“Human clusters i5, i7, i1, i4, and i3 matched mouse Smad3+ and Ndnf+ clusters. Clusters i6, i8, i9, i11, and i10 matched mouse Vip+ clusters, and cluster i2 matched mouse Sst+ clusters.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Rosehip cells: novel morphological features in layer 1 of the human cerebral cortex
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
“Membrane properties of human neurons did not show significant changes for up to 20 h after slicing”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Methods > Electrophysiological recordings
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
“In contrast, RCs are CCK-positive but cannabinoid receptor-negative, and appear to selectively target distal dendrites of pyramidal neurons.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Discussion
hedgedcorrelational- 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
“confirming that transcriptomic clusters were consistent between donors and not driven by technical artifacts.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Methods > Statistics
boostedn = 2- 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 total of 408 GAD1+ cells were identified from two individuals for this quantification.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Methods > Multiplex fluorescent in situ hybridization (FISH)
plainn = 2- 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.
None of the sources cited for this claim have been checked yet.
In the paper
“Indeed there is evidence for significant neuronal differences between rodents and human; for example, distinct membrane8,9 and synaptic10–14 properties and dendritic complexity15–17 of human neurons might contribute to human specific signal processing.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Abstract
What the sources say
- Not checked yetcites [8] Eyal, G. et al. Unique membrane properties and enhanced signal processing in human neocortical neurons. eLife 5, e16553 (2016). source
- Not checked yetcites [9] Wang, B. et al. A subtype of inhibitory interneuron with intrinsic persistent activity in human and monkey neocortex. Cell Rep. 10, 1450–1458 (2015). source
- Not checked yetcites [10] Molnár, G. et al. Complex events initiated by individual spikes in the human cerebral cortex. PLoS Biol. 6, e222 (2008). source
- Not checked yetcites [11] Molnár, G. et al. Human pyramidal to interneuron synapses are mediated by multi-vesicular release and multiple docked vesicles. eLife 5, e18167 (2016). source
- Not checked yetcites [12] Testa-Silva, G. et al. Human synapses show a wide temporal window for spike-timing-dependent plasticity. Front. Synaptic Neurosci. 2, 12 (2010).
- Not checked yetcites [13] Verhoog, M. B. et al. Mechanisms underlying the rules for associative plasticity at adult human neocortical synapses. J. Neurosci. 33, 17197–17208 (2013). source
- Not checked yetcites [14] Szegedi, V. et al. Plasticity in single axon glutamatergic connection interneurons regulates complex events in the human neocortex to GABAergic. PLoS Biol. 14, e2000237 (2016). source
- Not checked yetcites [15] Elston, G. N. Pyramidal cells of the frontal lobe: all the more spinous to think with. J. Neurosci. 20, RC95 (2000). source
- Not checked yetcites [16] Morales, J. et al. Random positions of dendritic spines in human cerebral cortex. J. Neurosci. 34, 10078–10084 (2014). source
- Not checked yetcites [17] Mohan, H. et al. Dendritic and axonal architecture of individual pyramidal neurons across layers of adult human neocortex. Cereb. Cortex 25, 4839–4853 (2015). source
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.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Recent systematic efforts have provided insight into the cellular composition and organization of rodent neocortical circuits, suggesting the presence of several dozen inhibitory and excitatory cell types3–5,7.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Abstract
What the sources say
- Not checked yetcites [3] Markram, H. et al. Reconstruction and simulation of neocortical microcircuitry. Cell 163, 456–492 (2015). source
- Not checked yetcites [4] Tasic, B. et al. Adult mouse cortical cell taxonomy revealed by single cell transcriptomics. Nat. Neurosci. 19, 335–346 (2016). source
- Not checked yetcites [5] Zeisel, A. et al. Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq. Science 347, 1138–1142 (2015). source
- Not checked yetcites [7] Jiang, X. et al. Principles of connectivity among morphologically defined cell types in adult neocortex. Science 350, aac9462 (2015). source
hedged- 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
“Together, these data strongly link the anatomically-defined rosehip phenotype with a highly distinctive transcriptomic cell type signature that is found in human but apparently not in mouse layer 1.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Rosehip cells: novel morphological features in layer 1 of the human cerebral cortex
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 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
“Although the transcriptomic comparison is between human temporal cortex and mouse visual cortex, regional differences seem unlikely to account for this difference as we found the anatomically defined rosehip type in multiple human regions.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Discussion
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.
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
“Quantification of cell proportions using marker expression is complicated by two factors; first, markers for one cell type are often expressed in others, and second, individual markers are often not expressed in every cell in a cluster.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Rosehip cells: novel morphological features in layer 1 of the human cerebral cortex
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.
In the paper
“It is widely accepted28 that CCK-positive cells in the rodent show selectively high expression of cannabinoid receptors and are involved in perisomatic inhibition.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Discussion
What the sources say
- Not checked yetcites [28] Katona, I. & Freund, T. F. Multiple functions of endocannabinoid signaling in the brain. Annu. Rev. Neurosci. 35, 529–558 (2012). source
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.
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, local inputs to RCs appear to be predominantly GABAergic, acknowledging that some axon collaterals of pyramidal cells were cut during the slicing procedure (Fig.5C) leading to a potential underrepresentation of pyramidal cell triggered EPSPs.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Function of rosehip cells in local microcircuits
hedgeddirect- 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 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
“Together these approaches provide convergent evidence for robust cell type identities and concomitant evidence for species conservation or specialization.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > 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: 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
“Specimens were further screened for RNA quality and had an RNA integrity number (RIN) ≥7.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Methods > Postmortem human brain specimens
plainn = 2- 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.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“All human specimens were controls (nonpathological) and were therefore allocated into the same experimental group.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Methods > Statistics
plainn = 2- 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.
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
“Positive controls (10 nuclei pools and/or 10 pg and 1 pg total RNA) were included on every 96-well plate of sorted nuclei.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Methods > Nuclei isolation and FACS
plain- 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.
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 this Random Forest classification model, all 196 samples in the training set were classified correctly with high confidence scores.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Methods > RNA-Seq quality control
plainn = 196- 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.
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
“Sweeps were discarded with less than 5 spikes for the calculation of ISI SD.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Methods > Firing classification analysis
plain- 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
“Action potentials backpropagate to distal dendrites of human pyramidal cells and can be attenuated by RC activation.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Discussion
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
“Application of the random forest model to these test Pass and Fail samples resulted in only 8 misclassifications (4.9%), for a classification accuracy of 95%.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Methods > RNA-Seq quality control
plainn = 185- 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.
None of the sources cited for this claim have been checked yet.
In the paper
“our sample sizes are similar to those reported in previous publications10,11,14.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Methods > Statistics
What the sources say
- Not checked yetcites [10] Molnár, G. et al. Complex events initiated by individual spikes in the human cerebral cortex. PLoS Biol. 6, e222 (2008). source
- Not checked yetcites [11] Molnár, G. et al. Human pyramidal to interneuron synapses are mediated by multi-vesicular release and multiple docked vesicles. eLife 5, e18167 (2016). source
- Not checked yetcites [14] Szegedi, V. et al. Plasticity in single axon glutamatergic connection interneurons regulates complex events in the human neocortex to GABAergic. PLoS Biol. 14, e2000237 (2016). source
plainn = 2- 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.
None of the sources cited for this claim have been checked yet.
In the paper
“The bouton morphology and/or the compact axonal field of RCs resembles that of cell types described in deeper layers of the cat cortex that innervate relatively proximal dendrites (dendrite targeting and clutch cells)40,41.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Discussion
What the sources say
- Not checked yetcites [40] Tamás, G., Buhl, E. H. & Somogyi, P. Fast IPSPs elicited via multiple synaptic release sites by different types of GABAergic neuron in the cat visual cortex. J. Physiol. (Lond.) 500, 715–738 (1997). source
- Not checked yetcites [41] Kisvárday, Z. F., Martin, K. A. C., Whitteridge, D. & Somogyi, P. Synaptic connections of intracellularly filled clutch cells: a type of small basket cell in the visual cortex of the cat. J. Comp. Neurol. 241, 111–137 (1985). source
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.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Data collection and analysis were not performed blind to the conditions of the experiments.”
- Also stated in: § Statistics · plain
“data collection and analysis were not performed blind to the conditions of the experiments.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Methods > Electrophysiological recordings
plain- 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.
- Also stated in: § Statistics · plain
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
“In total, 443/470 (94.3%) of nuclei were defined as core.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Methods > Cluster visualization
plain- 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
“Positive controls (POLR2A, UBC and PPIB) were used on each tissue sample to ensure RNA quality (ACD Bio, 320861).”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Methods > Multiplex fluorescent in situ hybridization (FISH)
What the sources say
- Not checked yetcites ACD Bio, 320861
plain- 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.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“The tissue specimens used in this study were pre-screened for known neuropsychiatric and neuropathological history, and underwent routine serological testing and toxicology screening.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Methods > Postmortem human brain specimens
plain- 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.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“No data with successful quality control were excluded from the analyses.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Methods > Statistics
plainn = 2- 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.
None of the sources cited for this claim have been checked yet.
In the paper
“The sharp resonance in the theta-range detected in individual RCs and its potential spread through gap junctions to a rosehip network could phase-selectively interact with long range inputs similarly to mechanisms suggested for example in oscillation dependent memory consolidation30,46.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Discussion
What the sources say
- Not checked yetcites [30] Freund, T. F. & Buzsáki, G. Interneurons of the hippocampus. Hippocampus 6, 347–470 (1996). source
- Not checked yetcites [46] Klausberger, T. & Somogyi, P. Neuronal diversity and temporal dynamics: the unity of hippocampal circuit operations. Science 321, 53–57 (2008). source
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: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“recordings included in the analysis were arbitrarily terminated 15 h after slice preparation.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Methods > Electrophysiological recordings
plain- 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.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“All tissue collection was performed in accordance with the provisions of the Uniform Anatomical Gift Act described in Health and Safety Code §§ 7150, et seq., and other applicable state and federal laws and regulations.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Methods > Postmortem human brain specimens
plain- 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.
None of the sources cited for this claim have been checked yet.
In the paper
“A better understanding of human cellular and circuit organization may help counteract the current lack of success in translating promising rodent results to effective treatment against human neuropsychiatric disorders49,50.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Discussion
What the sources say
- Not checked yetcites [49] Mak, I. W., Evaniew, N. & Ghert, M. Lost in translation: animal models and clinical trials in cancer treatment. Am. J. Transl. Res. 6, 114–118 (2014).
- Not checked yetcites [50] Cavanaugh, S. E., Pippin, J. J. & Barnard, N. D. Animal models of Alzheimer disease: historical pitfalls and a path forward. ALTEX 31, 279–302 (2014). source
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: fails — It may be too vague to check 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. It may be too vague to check against evidence. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“The uniquely small membrane capacitance (Cm) found in human pyramidal cells8 promotes backpropagation of action potentials and increases excitability in human dendrites13,29 relative to rodent dendrites having larger Cm.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Discussion
What the sources say
- Not checked yetcites [8] Eyal, G. et al. Unique membrane properties and enhanced signal processing in human neocortical neurons. eLife 5, e16553 (2016). source
- Not checked yetcites [13] Verhoog, M. B. et al. Mechanisms underlying the rules for associative plasticity at adult human neocortical synapses. J. Neurosci. 33, 17197–17208 (2013). source
- Not checked yetcites [29] Kerekes, B. P. et al. Combined two-photon imaging, electrophysiological, and anatomical investigation of the human neocortex in vitro. Neurophotonics 1, 011013 (2014). source
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.
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
“The function of neuron types specific to the human circuit could be important in understanding pathological alterations of network functions.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Discussion
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: fails — It may be too vague to check 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. It may be too vague to check against evidence. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“No sample-size calculation was performed”
- Also stated in: § Statistics · plain
“No statistical methods were used to pre-determine sample sizes”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Methods > Statistics
plain- 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.
- Also stated in: § Statistics · plain
In the paper
“To remove data from low quality nuclei samples prior to downstream analysis, we implemented a Random Forest machine learning classification approach as described in detail in Aevermann et al. 58.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Methods > RNA-Seq quality control
What the sources say
- Not checked yetcites [58] Aevermann, B. et al. Production of a preliminary quality control pipeline for single nuclei RNA-seq and its application in the analysis of cell type diversity of post-mortem human brain neocortex. Pac. Symp. Biocomput. 22, 564–575 (2017).
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.
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 assess the robustness of clusters, the iterative clustering procedure described above was repeated 100 times for random subsamples of 80% of nuclei.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Methods > Clustering nuclei
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.
In the paper
“Data from low quality nuclei samples was removed prior to downstream analysis, using a Random Forest machine learning classification approach as described58.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Methods > Statistics
What the sources say
- Not checked yetcites [58] Aevermann, B. et al. Production of a preliminary quality control pipeline for single nuclei RNA-seq and its application in the analysis of cell type diversity of post-mortem human brain neocortex. Pac. Symp. Biocomput. 22, 564–575 (2017).
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.
None of the sources cited for this claim have been checked yet.
In the paper
“Addition of new human cell types, or specialization of existing types through major modification of cellular features, would be expected to alter circuit function3,43,44, and therefore cannot be studied in rodents.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Discussion
What the sources say
- Not checked yetcites [3] Markram, H. et al. Reconstruction and simulation of neocortical microcircuitry. Cell 163, 456–492 (2015). source
- Not checked yetcites [43] 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 [44] Gjorgjieva, J., Drion, G. & Marder, E. Computational implications of biophysical diversity and multiple timescales in neurons and synapses for circuit performance. Curr. Opin. Neurobiol. 37, 44–52 (2016). source
hedgeddirect- 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
“reactions having CT values less than 23 or greater than 33 were considered primer dimers or background signals, respectively, and excluded from the data set.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Methods > Single cell reverse transcription and digital PCR
plain- 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.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“The Western Institutional Review Board reviewed tissue collection processes and determined that they did not constitute human subjects research requiring IRB review.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Methods > Postmortem human brain specimens
plain- 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.
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
“Randomization was not used.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Methods > Statistics
plain- 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.
None of the sources cited for this claim have been checked yet.
In the paper
“For example, several highly selective markers for RCs have been implicated as risk factors for neuropsychiatric disease, including netrin G1 (NTNG1) for Rett syndrome47 and neurotrypsin (PRSS12) for mental retardation48.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Discussion
What the sources say
- Not checked yetcites [47] Borg, I. et al. Disruption of Netrin G1 by a balanced chromosome translocation in a girl with Rett syndrome. Eur. J. Hum. Genet. 13, 921–927 (2005). source
- Not checked yetcites [48] Molinari, F. et al. Truncating neurotrypsin mutation in autosomal recessive nonsyndromic mental retardation. Science 298, 1779–1781 (2002). 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. It may state two separate claims as one.
In the paper
“Moreover, when assessing layer 1 canonical inhibitory pathways in rodent with high throughput electrophysiology capable of sampling all cell types in layer 1, Lee at al.42 found two interneuron types and two canonical pathways involving feed forward interneuron-to-interneuron connections.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Discussion
What the sources say
- Not checked yetcites [42] Lee, A. J. et al. Canonical organization of layer 1 neuron-led cortical inhibitory and disinhibitory interneuronal circuits. Cereb. Cortex 25, 2114–2126 (2015). source
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.
In the paper
“Furthermore, focal intralayer inhibition restricted by the compact axonal arbor of RCs to distal dendrites of a column of pyramidal cells is also missing from the rodent; rather, mouse feedforward inhibitory connections are vertically spread to all somatodendritic domains42.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Discussion
What the sources say
- Not checked yetcites [42] Lee, A. J. et al. Canonical organization of layer 1 neuron-led cortical inhibitory and disinhibitory interneuronal circuits. Cereb. Cortex 25, 2114–2126 (2015). source
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.
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
“Patients with a history of epilepsy were excluded from this study.”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Methods > Electrophysiological recordings
plain- 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.
The authors state this as an assumption.
Conservation of cellular and circuit principles in human cortex is assumed but largely untested.
“However, conservation of cellular and circuit principles in human cortex is assumed but largely untested to date.”
The paper relies on this without support.
Layer 1 of the middle temporal gyrus is expected to predominantly contain inhibitory neurons.
“microdissected layer 1 of the middle temporal gyrus, expected to predominantly contain inhibitory neurons”
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?
In the citing paper
“The cellular organization of interneuron diversity is remarkably similar between mouse and human, but there are important differences in the morphology, gene expression, laminar distribution and proportions of certain types of interneurons (Boldog et al., 2018; DeFelipe, 1997; Hodge et al., 2018).”
From Development and Functional Diversification of Cortical Interneurons (2018) · cites this paper as Boldog et al., 2018
In the citing paper
“these cells are expected to have the Sst-Chodl t-type, linked to deep long-range projecting interneurons12,14,36,37 (Fig. 7h).”
From Classification of electrophysiological and morphological neuron types in the mouse visual cortex (2019) · cites this paper as [36]
In the citing paper
“Notably, this approach provides the means to evaluate and compare the circuit contributions and function of PV cINs across species, regardless of their genetic accessibility44,45.”
From Viral manipulation of functionally distinct interneurons in mice, non-human primates and humans (2020) · cites this paper as [45]
In the citing paper
“A small sample size in a single cell genomics study does affect statistical power, but does not preclude the possibility of drawing meaningful inferences of cell type gene expression in the human brain (9,41) .”
From Single cell transcriptome profiling of the human alcohol-dependent brain (2020) · cites this paper as [41]
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.
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
“postsynaptic dendrites (n=46) revealed dendritic spines and sparse innervation by symmetrical synapses on the shaft, suggesting that these dendrites belonged to pyramidal cells (n=41, 86%, Fig.5J).”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Function of rosehip cells in local microcircuits
Reported 86 · recomputed 89.130435
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Results > Intrinsic electrophysiological properties of rosehip cells
“time constants of RCs (7.3±3.7 ms) were similar to neurogliaform (8.9±2.4 ms, p<0.001)”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Methods > Electrophysiological recordings
“differences were considered significant if p<0.05.”
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
“Template cDNA was supplemented with nuclease free water to a final volume of 8 μl. 2 μl TaqMan Assays (Thermo Fisher), 10 μl OpenArray Digital PCR Master Mix (Thermo Fisher, Cat.No.: 4458095) and nuclease free water (3 μl) were mixed to obtain a total volume of 20 μl”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Methods > Single cell reverse transcription and digital PCR
Reported 20 · recomputed 23
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Methods > Measurement of impedance profile
“For statistical comparison of the impedance profiles, four parameters were considered:”
§ Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type > Methods > Measurement of impedance profile
“impedance at lowest frequency (Z0.2Hz); resonance magnitude (Q, the impedance magnitude at the resonance peak i.e. maximal impedance value divided by the impedance magnitude at the lowest input frequency of 0.2 Hz); and the frequency at maximum impedance (fmax).”
Citations
Cites
R: A Language and Environment for Statistical Computing
R Core Team (2000) · doi:10.32614/r.manuals · Cited by 355,893
Trimmomatic: a flexible trimmer for Illumina sequence data
Bolger, A. M., Lohse, M., & Usadel, B. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu170 · Cited by 65,548
Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp616 · Cited by 41,364
limma powers differential expression analyses for RNA-sequencing and microarray studies
Ritchie, M. E., Phipson, B., Wu, D., Hu, Y., Law, C. W., Shi, W., & Smyth, G. K. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv007 · Cited by 40,458
(2008) · Journal of Machine Learning Research · Cited by 33,051
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
Li, B., & Dewey, C. N. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-323 · Cited by 22,179
HTSeq—a Python framework to work with high-throughput sequencing data
Anders, S., Pyl, P. T., & Huber, W. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btu638 · Cited by 21,464
(1996) · Cited by 20,179
The mouse brain in stereotaxic coordinates
Konsman, J. (2003) · Psychoneuroendocrinology · doi:10.1016/s0306-4530(03)00088-x · Cited by 16,796
The Mouse Brain in Stereotaxic Coordinates
Paxinos, G. (2001) · Cited by 12,859
Cited by
Sorted by citations
Conserved cell types with divergent features in human versus mouse cortex
Hodge, R. D., Bakken, T. E., Miller, J. A., Smith, K. A., Barkan, E. R., Graybuck, L. T., Close, J. L., Long, B., Johansen, N., Penn, O., et al. (2019) · Nature · doi:10.1038/s41586-019-1506-7 · Cited by 1,775
Self-citationComparative cellular analysis of motor cortex in human, marmoset and mouse
Bakken, T. E., Jorstad, N. L., Hu, Q., Lake, B. B., Tian, W., Kalmbach, B. E., Crow, M., Hodge, R. D., Krienen, F. M., Sorensen, S. A., et al. (2021) · Nature · doi:10.1038/s41586-021-03465-8 · Cited by 812
Self-citationDevelopment and Functional Diversification of Cortical Interneurons
Lim, L., Mi, D., Llorca, A., & Marín, O. (2018) · Neuron · doi:10.1016/j.neuron.2018.10.009 · Cited by 714
Dendritic action potentials and computation in human layer 2/3 cortical neurons
Gidon, A., Zolnik, T. A., Fidzinski, P., Bolduan, F., Papoutsi, A., Poirazi, P., Holtkamp, M., Vida, I., & Larkum, M. E. (2020) · Science · doi:10.1126/science.aax6239 · Cited by 599
Classification of electrophysiological and morphological neuron types in the mouse visual cortex
Gouwens, N. W., Sorensen, S. A., Berg, J., Lee, C., Jarsky, T., Ting, J., Sunkin, S. M., Feng, D., Anastassiou, C. A., Barkan, E., et al. (2019) · Nature Neuroscience · doi:10.1038/s41593-019-0417-0 · Cited by 456
Self-citationDevelopment and arealization of the cerebral cortex
Cadwell, C. R., Bhaduri, A., Mostajo-Radji, M. A., Keefe, M. G., & Nowakowski, T. J. (2019) · Neuron · doi:10.1016/j.neuron.2019.07.009 · Cited by 408
Innovations in Primate Interneuron Repertoire
Krienen, F. M., Goldman, M., Zhang, Q., del Rosario, R., Florio, M., Machold, R., Saunders, A., Levandowski, K., Zaniewski, H., Schuman, B., et al. (2019) · doi:10.1101/709501 · Cited by 372
Innovations present in the primate interneuron repertoire
Krienen, F. M., Goldman, M., Zhang, Q., C. H. del Rosario, R., Florio, M., Machold, R., Saunders, A., Levandowski, K., Zaniewski, H., Schuman, B., et al. (2020) · Nature · doi:10.1038/s41586-020-2781-z · Cited by 381
Madison, A. A., & Kiecolt‐Glaser, J. K. (2019) · Current Opinion in Behavioral Sciences · doi:10.1016/j.cobeha.2019.01.011 · Cited by 383
“However, humans diverge from rodents in many relevant ways, such as neuronal expression [56] and even gut microbiota [57], underscoring the need for more clinical research to replicate and extend preclinical research.”
Macroscopic gradients of synaptic excitation and inhibition in the neocortex
Wang, X. (2020) · Nature reviews. Neuroscience · doi:10.1038/s41583-020-0262-x · Cited by 289
Illuminating dendritic function with computational models
Poirazi, P., & Papoutsi, A. (2020) · Nature reviews. Neuroscience · doi:10.1038/s41583-020-0301-7 · Cited by 313
Large-scale neural recordings with single neuron resolution using Neuropixels probes in human cortex
Paulk, A. C., Kfir, Y., Khanna, A. R., Mustroph, M. L., Trautmann, E. M., Soper, D. J., Stavisky, S. D., Welkenhuysen, M., Dutta, B., Shenoy, K. V., et al. (2022) · Nature Neuroscience · doi:10.1038/s41593-021-00997-0 · Cited by 283
“These results suggest that the ultra-high-density recording approach enabled by Neuropixels might enable an association of electrophysiologically identified units with specific neuronal subtypes 50,51 .”
ResultViral manipulation of functionally distinct interneurons in mice, non-human primates and humans
Vormstein-Schneider, D., Lin, J. D., Pelkey, K. A., Chittajallu, R., Guo, B., Arias-Garcia, M. A., Allaway, K., Sakopoulos, S., Schneider, G., Stevenson, O., et al. (2020) · Nature Neuroscience · doi:10.1038/s41593-020-0692-9 · Cited by 235
Connectomic comparison of mouse and human cortex
Loomba, S., Straehle, J., Gangadharan, V., Heike, N., Khalifa, A., Motta, A., Ju, N., Sievers, M., Gempt, J., Meyer, H. S., et al. (2022) · Science · doi:10.1126/science.abo0924 · Cited by 242
Herring, C. A., Simmons, R. K., Freytag, S., Poppe, D., Moffet, J. J. D., Pflueger, J., Buckberry, S., Vargas-Landín, D. B., Clément, O., Goñi, E., et al. (2022) · Cell · doi:10.1016/j.cell.2022.09.039 · Cited by 242
“Marker Genes - RELN (Overstreet-Wadiche and McBain, 2015), SV2C (Boldog et al., 2018), KIT (Mickelsen et al., 2019), CXCL14 (Boldog et al., 2018), LAMP5 (Mickelsen et al., 2019), CCK (Lake et al., 2018).”
BackgroundHuman brain organogenesis: Toward a cellular understanding of development and disease
Kelley, K. W., & Pașca, S. P. (2021) · Cell · doi:10.1016/j.cell.2021.10.003 · Cited by 244
“Similarly, single-nucleus transcriptomics coupled with detailed morphological and electrophysiological analyses identified a ‘‘rosehip’’ shaped GABAergic interneuron located in human cortical layer 1 without a mouse homolog (Boldog et al., 2018).”
BackgroundMouse and human share conserved transcriptional programs for interneuron development
Shi, Y., Wang, M., Mi, D., Lu, T., Wang, B., Dong, H., Zhong, S., Chen, Y., Sun, L., Zhou, X., et al. (2021) · Science · doi:10.1126/science.abj6641 · Cited by 196
Rewiring of human neurodevelopmental gene regulatory programs by human accelerated regions
Girskis, K. M., Stergachis, A. B., DeGennaro, E. M., Doan, R. N., Qian, X., Johnson, M. B., Wang, P. P., Sejourne, G. M., Nagy, M. A., Pollina, E. A., et al. (2021) · Neuron · doi:10.1016/j.neuron.2021.08.005 · Cited by 193
“Longer cell cycles are thought to reduce the rate of somatic mutation or maintain DNA quality control and may facilitate formation of the remarkable diversity of neuronal types that constitute the human brain (Boldog et al., 2018; Hodge et al., 2019), but they come at the potential cost of increasing heterochrony, a l…”
BackgroundInterneuron Types as Attractors and Controllers
Fishell, G., & Kepecs, Á. (2019) · Annual Review of Neuroscience · doi:10.1146/annurev-neuro-070918-050421 · Cited by 212
“In addition, recent work has started to examine the related questions of how interneuron identities vary across brain regions (Saunders et al. 2018), as well as across species ranging from reptiles to humans (Boldog et al. 2018, Tosches et al. 2018), to understand how they emerged through evolution.”
BackgroundHuman Models Are Needed for Studying Human Neurodevelopmental Disorders
Zhao, X., & Bhattacharyya, A. (2018) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2018.10.009 · Cited by 192
“In fact, a new human interneuron subtype was recently identified with features never described in rodents.(80) Unique Genetics.”
BackgroundFunctional enhancer elements drive subclass-selective expression from mouse to primate neocortex
Mich, J. K., Graybuck, L. T., Hess, E. E., Mahoney, J. T., Kojima, Y., Ding, Y., Somasundaram, S., Miller, J. A., Kalmbach, B. E., Radaelli, C., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.108754 · Cited by 193
Self-citationSingle-cell-resolution transcriptome map of human, chimpanzee, bonobo, and macaque brains
Khrameeva, E., Kurochkin, I., Han, D., Guijarro, P., Kanton, S., Santel, M., Qian, Z., Rong, S., Mazin, P., Sabirov, M., et al. (2020) · Genome Research · doi:10.1101/gr.256958.119 · Cited by 162
“…sufficient to accurately examine expression evolution in specific neuronal subtypes, such as von Economo neurons, known to be overrepresented in human AC and the frontoinsular cortex (Yang et al. 2019), or the rosehip neurons present in human but not rodent cortical layer I (Boldog et al. 2018).”
BackgroundDevelopmental mechanisms underlying the evolution of human cortical circuits
Vanderhaeghen, P., & Polleux, F. (2023) · Nature Reviews Neuroscience · doi:10.1038/s41583-023-00675-z · Cited by 173
Single nucleus multi-omics identifies human cortical cell regulatory genome diversity
Luo, C., Liu, H., Xie, F., Armand, E. J., Siletti, K., Bakken, T. E., Fang, R., Doyle, W. I., Stuart, T., Hodge, R. D., et al. (2022) · Cell Genomics · doi:10.1016/j.xgen.2022.100107 · Cited by 173
Self-citationAstrocytes as Guardians of Neuronal Excitability: Mechanisms Underlying Epileptogenesis
Verhoog, Q. P., Holtman, L., Aronica, E., & van Vliet, E. A. (2020) · Frontiers in Neurology · doi:10.3389/fneur.2020.591690 · Cited by 149
“Numerous studies have been performed showing a plethora of astrocytic released gliotransmitters: (1) amino acids including glutamate (177–179), D-serine (180, 181), GABA (182–184) and glycine (185–187), (2) nucleotides, such as adenosine 5triphosphate (ATP) (188–190), (3) organic acids including lactate (191–193), tau…”
InfluentialNeocortical Layer 1: an elegant solution to top-down and bottom-up integration
Schuman, B., Dellal, S., Prönneke, A., Machold, R., & Rudy, B. (2021) · Annual Review of Neuroscience · doi:10.1146/annurev-neuro-100520-012117 · Cited by 148
Single-cell multi-cohort dissection of the schizophrenia transcriptome
Ruzicka, W. B., Mohammadi, S., Fullard, J. F., Dávila-Velderrain, J., Subburaju, S., Tso, D. R., Hourihan, M., Jiang, S., Lee, H.-C., Bendl, J. M., et al. (2024) · Science · doi:10.1126/science.adg5136 · Cited by 163
“[vasoactive intestinal peptide (VIP)+ and Reelin+], and two subpopulations of the recently described rosehip interneurons ( 32 ).”
BackgroundChang, C.-Y., Ting, H.-C., Liu, C.-A., Su, H., Chiou, T., Lin, S., Harn, H., & Ho, T. (2020) · Molecules · doi:10.3390/molecules25082000 · Cited by 140
Cell type-specific epigenetic links to schizophrenia risk in the brain
Mendizabal, I., Berto, S., Usui, N., Toriumi, K., Chatterjee, P., Douglas, C., Huh, I., Jeong, H., Layman, T. S., Tamminga, C. A., et al. (2019) · Genome biology · doi:10.1186/s13059-019-1747-7 · Cited by 107
Signature morphoelectric properties of diverse GABAergic interneurons in the human neocortex
Lee, B. R., Dalley, R., Miller, J. A., Chartrand, T., Close, J., Mann, R., Mukora, A., Ng, L., Alfiler, L., Baker, K., et al. (2023) · Science · doi:10.1126/science.adf6484 · Cited by 125
Self-citationSchwarz, N., Uysal, B., Welzer, M., Bahr, J. C., Layer, N., Löffler, H., Stanaitis, K., Ashraf, H. P., Weber, Y. G., Hedrich, U. B. S., et al. (2019) · eLife · doi:10.7554/elife.48417 · Cited by 120
Single cell transcriptome profiling of the human alcohol-dependent brain
Brenner, E., Tiwari, G. R., Kapoor, M., Liu, Y., Brock, A., & Mayfield, R. D. (2020) · Human Molecular Genetics · doi:10.1093/hmg/ddaa038 · Cited by 118
Feng, G., Jensen, F. E., Greely, H. T., Okano, H., Treue, S., Roberts, A., Fox, J. G., Caddick, S. J., Poo, M.-M., Newsome, W. T., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2006515117 · Cited by 124
Evolution of cortical neurons supporting human cognition
Galakhova, A. A., Hunt, S., Wilbers, R., Heyer, D. B., de Kock, C. P. J., Mansvelder, H. D., & Goriounova, N. A. (2022) · Trends in Cognitive Sciences · doi:10.1016/j.tics.2022.08.012 · Cited by 127
Mossink, B., Negwer, M., Schubert, D., & Nadif Kasri, N. (2021) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-020-03714-5 · Cited by 114
“While mice have many advantages as model organisms and many features are conserved down to the cellular level [331], some features appear to be unique to the human lineage, for example specialized cell-types such as outer radial glia cells [448], subpial interlaminar astrocytes [449], or the recently described rosehip…”
BackgroundChameh, H. M., Rich, S., Wang, L., Chen, F., Zhang, L., Carlen, P. L., Tripathy, S. J., & Valiante, T. A. (2021) · Nature Communications · doi:10.1038/s41467-021-22741-9 · Cited by 110
Interneuron origin and molecular diversity in the human fetal brain
Yu, Y., Zeng, Z., Xie, D., Chen, R., Sha, Y., Huang, S., Cai, W., Chen, W., Li, W., Ke, R., et al. (2021) · Nature Neuroscience · doi:10.1038/s41593-021-00940-3 · Cited by 108
Hodge, R. D., Miller, J. A., Novotny, M. A., Kalmbach, B. E., Ting, J. T., Bakken, T. E., Aevermann, B. D., Barkan, E. R., Berkowitz-Cerasano, M. L., Cobbs, C., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-14952-3 · Cited by 95
Self-citationApplications of brain organoids in neurodevelopment and neurological diseases
Sun, N., Meng, X., Liu, Y., Song, D., Jiang, C., & Cai, J. (2021) · Journal of Biomedical Science · doi:10.1186/s12929-021-00728-4 · Cited by 103
Single-cell dissection of the human motor and prefrontal cortices in ALS and FTLD
Pineda, S. S., Lee, H., Fitzwalter, B. E., Mohammadi, S., Pregent, L., Gardashli, M., Mantero, J. C., Engelberg-Cook, E., DeJesus‐Hernandez, M., van Blitterswijk, M., et al. (2024) · Cell · doi:10.1016/j.cell.2024.02.031 · Cited by 158
Strong and reliable synaptic communication between pyramidal neurons in adult human cerebral cortex
Hunt, S., Leibner, Y., Mertens, E. J., Barros-Zulaica, N., Kanari, L., Heistek, T. S., Karnani, M., Aardse, R., Wilbers, R., Heyer, D. B., et al. (2022) · Cerebral Cortex · doi:10.1093/cercor/bhac246 · Cited by 84
Peng, Y., Mittermaier, F. X., Planert, H., Schneider, U. C., Alle, H., & Geiger, J. R. P. (2019) · eLife · doi:10.7554/elife.48178 · Cited by 93
Maynard, K. R., Tippani, M., Takahashi, Y., Phan, B. N., Hyde, T. M., Jaffe, A. E., & Martinowich, K. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa312 · Cited by 78
Common cell type nomenclature for the mammalian brain
Miller, J. A., Gouwens, N. W., Tasic, B., Collman, F., van Velthoven, C. T. J., Bakken, T. E., Hawrylycz, M., Zeng, H., Lein, E. S., & Bernard, A. (2020) · eLife · doi:10.7554/elife.59928 · Cited by 75
“Furthermore, functional properties observed in matched cell types may diverge across species (Bakken et al., 2020a; Berg et al., 2020; Boldog et al., 2018; Hodge et al., 2019) and as cells advance along trajectories of development (Nowakowski et al.”
BackgroundInfluentialSelf-citationEvolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse
Bakken, T. E., Jorstad, N. L., Hu, Q., Lake, B. B., Tian, W., Kalmbach, B. E., Crow, M., Hodge, R. D., Krienen, F. M., Sorensen, S. A., et al. (2020) · doi:10.1101/2020.03.31.016972 · Cited by 809
Self-citationChartrand, T., Dalley, R., Close, J., Goriounova, N. A., Lee, B. R., Mann, R., Miller, J. A., Molnar, G., Mukora, A., Alfiler, L., et al. (2023) · Science · doi:10.1126/science.adf0805 · Cited by 88
“Forfurtheranalysisofthesereferencetrans-criptomicdatasets,datawasrestrictedtoonly L1 and the adjacent layer (L2 in human, L2/3 in mouse), to be as selective as possible while not riskingthe exclusion ofL1/2 border cells in case of imprecise dissections.”
BackgroundInfluentialSelf-citationShared and derived features of cellular diversity in the human cerebral cortex
Miller, D. J., Bhaduri, A., Šestan, N., & Kriegstein, A. R. (2019) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2018.12.005 · Cited by 79
Neurons with Complex Karyotypes Are Rare in Aged Human Neocortex
Chronister, W. D., Burbulis, I. E., Wierman, M. B., Wolpert, M. J., Haakenson, M. F., Smith, A. C. B., Kleinman, J. E., Hyde, T. M., Weinberger, D. R., Bekiranov, S., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2018.12.107 · Cited by 75
“Single-cell transcriptomic approaches are beginning to comprehensively catalog human neuronal diversity (Lake et al., 2016; Nowakowski et al., 2017) and identify new subtypes of human neurons (Boldog et al., 2018).”
BackgroundA Tradeoff in the Neural Code across Regions and Species
Pryluk, R., Kfir, Y., Gelbard-Sagiv, H., Fried, I., & Paz, R. (2019) · Cell · doi:10.1016/j.cell.2018.12.032 · Cited by 74
Mouse models of neurodegeneration: Know your question, know your mouse
Fisher, E., & Bannerman, D. M. (2019) · Science Translational Medicine · doi:10.1126/scitranslmed.aaq1818 · Cited by 80
Accelerated evolution of oligodendrocytes in the human brain
Berto, S., Mendizabal, I., Usui, N., Toriumi, K., Chatterjee, P., Douglas, C., Tamminga, C. A., Preuss, T. M., Yi, S. V., & Konopka, G. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1907982116 · Cited by 78
“We next compared the human-specific genes with single-cell transcriptome data from human brain (20).”
BackgroundX-chromosome regulation and sex differences in brain anatomy
Raznahan, A., & Distèche, C. M. (2020) · Neuroscience & Biobehavioral Reviews · doi:10.1016/j.neubiorev.2020.10.024 · Cited by 69
Leveraging the Cell Ontology to classify unseen cell types
Wang, S., Pisco, A. O., McGeever, A., Brbić, M., Žitnik, M., Darmanis, S., Leskovec, J., Karkanias, J., & Altman, R. B. (2021) · Nature Communications · doi:10.1038/s41467-021-25725-x · Cited by 87
“OnClass is a Python-based open source package able to compute cell type similarities between the hierarchical structure of existing cell ontologies, such as the Cell Ontology 25 and the Allen Ontology 20,33 .”
MethodAmyloid Cascade Hypothesis for the Treatment of Alzheimer’s Disease: Progress and Challenges
Wu, T., Ding, L., Cheng, Y., Jiang, S., Riaz, M. W., Fu, N., Mou, C., Ye, M., & Zheng, Y. (2022) · Aging and Disease · doi:10.14336/ad.2022.0412 · Cited by 81
“Besides, some specialized features were confirmed in the human brain, such as the presence of interlaminar astrocytes and rosehip neurons and the expansion of superficial cortical layers [98-100].”
BackgroundCell type discovery using single-cell transcriptomics: implications for ontological representation
Aevermann, B. D., Novotny, M. A., Bakken, T. E., Miller, J. A., Diehl, A. D., Osumi-Sutherland, D., Lasken, R. S., Lein, E. S., & Scheuermann, R. H. (2018) · Human Molecular Genetics · doi:10.1093/hmg/ddy100 · Cited by 66
“For one of the inhibitory interneuron cell types defined in this study (i5), we were able to connect the distinct transcriptional profile with a previous cell type defined based on its unique cellular morphology—the Rosehip cell (14).”
BackgroundSelf-citationPerspectives on defining cell types in the brain
Mukamel, E. A., & Ngai, J. (2019) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2018.11.007 · Cited by 56
“In parallel, complementary data from human and non-human primates, though less comprehensive, will enable comparative and evolutionary perspectives on mammalian brain cell types [79,80].”
BackgroundThe Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution
Taylor, D. M., Aronow, B. J., Tan, K., Bernt, K. M., Salomonis, N., Greene, C. S., Frolova, A., Henrickson, S. E., Wells, A. D., Pei, L., et al. (2019) · Developmental Cell · doi:10.1016/j.devcel.2019.03.001 · Cited by 64
de Souza, D. G., Almeida, R. F., Souza, D. O., & Zimmer, E. R. (2019) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2019.04.002 · Cited by 70
Bak, A., Koch, H., van Loo, K. M. J., et al. (2024) · Journal of Neuroscience Methods · doi:10.1016/j.jneumeth.2023.110055 · Cited by 64
The cell-type underpinnings of the human functional cortical connectome
Zhang, X.-H., Anderson, K. M., Dong, H.-M., Chopra, S., Dhamala, E., Emani, P. S., Gerstein, M., Margulies, D. S., & Holmes, A. J. (2024) · Nature Neuroscience · doi:10.1038/s41593-024-01812-2 · Cited by 67
“From technologies characterizing multimodal features of single cells, such as patch-seq 35 , transcriptionally defined cell types demonstrate electrophysiological and morphological distinction 36,37 .”
Ruzicka, W. B., Mohammadi, S., Dávila-Velderrain, J., Subburaju, S., Tso, D. R., Hourihan, M., & Kellis, M. (2020) · medRxiv · doi:10.1101/2020.11.06.20225342 · Cited by 53
Gittings, L. M., Alsop, E. B., Antone, J., Singer, M., Whitsett, T. G., Sattler, R., & Keuren‐Jensen, K. R. V. (2023) · Acta Neuropathologica · doi:10.1007/s00401-023-02599-5 · Cited by 58
Activity-dependent tuning of intrinsic excitability in mouse and human neurogliaform cells
Chittajallu, R., Auville, K., Mahadevan, V., Lai, M., Hunt, S., Calvigioni, D., Pelkey, K. A., Zaghloul, K. A., & McBain, C. J. (2020) · eLife · doi:10.7554/elife.57571 · Cited by 54
“Interestingly, even with the number of conditioning APs far exceeding that required to induce BF in NGFCs (800 - 1500 APs; 30Hz), BF could not be elicited in superficial cortical and hippocampal INs that were not NGFCs (non-NGFCs), including the recently described human rosehip cell(Boldog et al., 2018) (26 and 37 non…”
BackgroundInfluentialNests of dividing neuroblasts sustain interneuron production for the developing human brain
Paredes, M. F., Mora, C., Flores-Ramirez, Q., Cebrián‐Silla, A., Dosso, A. D., Larimer, P., Chen, J., Kang, G., González-Granero, S., Garcia, E., et al. (2022) · Science · doi:10.1126/science.abk2346 · Cited by 50
How can artificial neural networks approximate the brain?
Shao, F., & Shen, Z. (2023) · Frontiers in Psychology · doi:10.3389/fpsyg.2022.970214 · Cited by 66
Huang, A. Y., Li, P., Rodin, R. E., Kim, S. N., Dou, Y., Kenny, C. J., Akula, S. K., Hodge, R. D., Bakken, T. E., Miller, J. A., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2006163117 · Cited by 50
“1H) shows that they identified similar major cell types, with cells clustering by cell type rather than by platform, although the SMART-seq dataset from MTG defined finer subdivisions of cell type, as expected, because of its larger sample size and deeper sequence depth.”
BackgroundResultInfluentialSelf-citationUnraveling mechanisms of human brain evolution
Lancaster, M. A. (2024) · Cell · doi:10.1016/j.cell.2024.08.052 · Cited by 58
Szegedi, V., Paizs, M., Baka, J., Barzó, P., Molnár, G., Tamás, G., & Lamsa, K. P. (2020) · eLife · doi:10.7554/elife.51691 · Cited by 45
Self-citationMicroscale Physiological Events on the Human Cortical Surface
Paulk, A. C., Yang, J. C., Cleary, D. R., Soper, D. J., Halgren, M., O’Donnell, A. R., Lee, S., Ganji, M., Ro, Y. G., Oh, H., et al. (2021) · Cerebral Cortex · doi:10.1093/cercor/bhab040 · Cited by 47
Apical amplification—a cellular mechanism of conscious perception?
Marvan, T., Polák, M., Bachmann, T., & Phillips, W. A. (2021) · Neuroscience of Consciousness · doi:10.1093/nc/niab036 · Cited by 45
Distinctive Structural and Molecular Features of Myelinated Inhibitory Axons in Human Neocortex
Micheva, K. D., Chang, E. F., Nana, A. L., Seeley, W. W., Ting, J. T., Cobbs, C., Lein, E. S., Smith, S. J., Weinberg, R. J., & Madison, D. V. (2018) · eNeuro · doi:10.1523/eneuro.0297-18.2018 · Cited by 44
“For example, recent studies revealed two new interneuron types in human cortex that are not present in mouse cortex, and both of these interneurons are enriched in layer 1 (Boldog et al., 2018; Hodge et al., 2018).”
Human Brain Organoid Models of Developmental Epilepsies
Nieto‐Estévez, V., & Hsieh, J. (2020) · Epiliepsy currents/Epilepsy currents · doi:10.1177/1535759720949254 · Cited by 44
“Moreover, specific interneuron subtypes can be observed only in humans.(30) Many of these aspects of brain development can be recapitulated in organoids.”
BackgroundLayer 1 neocortex: Gating and integrating multidimensional signals
Huang, S., Wu, S. J., Sansone, G., Ibrahim, L. A., & Fishell, G. (2023) · Neuron · doi:10.1016/j.neuron.2023.09.041 · Cited by 43
Kim, M.-H., Radaelli, C., Thomsen, E. R., Monet, D., Chartrand, T., Jorstad, N. L., Mahoney, J. T., Taormina, M. J., Long, B., Baker, K. S., et al. (2023) · eLife · doi:10.7554/elife.81863 · Cited by 46
“…human neocortical slices derived from surgical resections ( Molnár et al., 2008 ; Jiang et al., 2012 ; Testa-Silva et al., 2014 ; Kalmbach et al., 2018 ; Beaulieu-Laroche et al., 2018 ; Boldog et al., 2018 ; Seeman et al., 2018 ; Peng et al., 2019 ; Planert et al., 2021 ; Campagnola et al., 2021 ).”
Self-citationA single-cell multi-omic atlas spanning the adult rhesus macaque brain
Chiou, K. L., Huang, X., Bohlen, M. O., Tremblay, S., DeCasien, A. R., O’Day, D. R., Spurrell, C. H., Gogate, A. A., Zintel, T. M., Andrews, M. G., et al. (2023) · Science Advances · doi:10.1126/sciadv.adh1914 · Cited by 44
Jouhanneau, J.-S., & Poulet, J. F. A. (2019) · Frontiers in Synaptic Neuroscience · doi:10.3389/fnsyn.2019.00015 · Cited by 38
“For example using single-cell RNA sequencing (Jiang et al., 2015; Cadwell et al., 2016; Fuzik et al., 2016; Muñoz et al., 2017; Boldog et al., 2018) or higher resolution bright field (Feldmeyer et al.”
MethodCapogna, M., Castillo, P. E., & Maffei, A. (2020) · European Journal of Neuroscience · doi:10.1111/ejn.14907 · Cited by 45
“This diversity is probably even more pronounced in the human cerebral cortex, where GABAergic cell types without apparent homology with rodent cortical cell types have been found (Boldog et al., 2018).”
BackgroundTai, D. J. C., Razaz, P., Erdin, S., Gao, D., Wang, J. P., Nuttle, X., de Esch, C. E., Collins, R. L., Currall, B., O’Keefe, K., et al. (2022) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2022.08.012 · Cited by 39
Single-cell profiling of the human primary motor cortex in ALS and FTLD
Pineda, S. S., Lee, H., Fitzwalter, B. E., et al. (2021) · bioRxiv · doi:10.1101/2021.07.07.451374 · Cited by 33
Comprehensive in situ mapping of human cortical transcriptomic cell types
Langseth, C. M., Gyllborg, D., Miller, J. A., Close, J., Long, B., Lein, E. S., Hilscher, M. M., & Nilsson, M. F. (2021) · Communications Biology · doi:10.1038/s42003-021-02517-z · Cited by 33
Self-citationKeefe, F., Monzón‐Sandoval, J., Rosser, A., Webber, C., & Li, M. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24098122 · Cited by 38
Stephan, M., Volkmann, P., & Rossner, M. J. (2019) · Dialogues in Clinical Neuroscience · doi:10.31887/dcns.2019.21.3/mrossner · Cited by 39
Cerebellar nuclei evolved by repeatedly duplicating a conserved cell type setPreprint
Kebschull, J. M., Ringach, N., Richman, E. B., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.06.25.170118 · Cited by 38
Molecular profiling of single neurons of known identity in two ganglia from the crab Cancer borealis
Northcutt, A. J., Kick, D. R., Otopalik, A. G., Goetz, B. M., Harris, R. M., Santin, J. M., Hofmann, H. A., Marder, E., & Schulz, D. J. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1911413116 · Cited by 33
Species-Specific miRNAs in Human Brain Development and Disease
Prodromidou, K., & Matsas, R. (2019) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2019.00559 · Cited by 38
“Similarly, a specialized GABAergic neuron subtype has recently been identified with a molecular and anatomical signature specific to humans (Boldog et al., 2018).”
BackgroundMedalla, M., Mo, B., Nasar, R. T., Zhou, Y., Park, J., & Luebke, J. I. (2023) · The Journal of Comparative Neurology · doi:10.1002/cne.25514 · Cited by 33
“…profiles, extrinsic factors such as laminar location, connectivity,andactivityplayakeyroleindeterminingthefunctionofdistinct interneuron types, and ultimately shaping the cortical inhibitory circuits that underlie behavior (Boldog et al., 2018; Bugeon et al., 2022; Pouchelon et al., 2021).”
BackgroundLayer 1 NDNF interneurons are specialized top-down master regulators of cortical circuits
Hartung, J., Schroeder, A., Vázquez, R. A. P., Poorthuis, R. B., & Letzkus, J. J. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.114212 · Cited by 36
Trutzer, I. M., García‐Cabezas, M. Á., & Zikopoulos, B. (2019) · Acta Neuropathologica Communications · doi:10.1186/s40478-019-0684-8 · Cited by 33
Machine learning for cell type classification from single nucleus RNA sequencing data
Le, H. Q., Peng, B., Uy, J., Carrillo, D., Zhang, Y., Aevermann, B. D., & Scheuermann, R. H. (2022) · PLoS ONE · doi:10.1371/journal.pone.0275070 · Cited by 30
“For example, snRNA-seq allowed for the identification of a specialized “rosehip” GABAergic neuron in human cortical layer 1 of the middle temporal gyrus with gap junctions that target apical dendritic shafts of layer 3 pyramidal neurons to inhibit back propagation of action potentials [4].”
BackgroundSelf-citationHan, X., Guo, S., Ji, N., Li, T., Liu, J., Ye, X., Wang, Y., Yun, Z., Xiong, F., Rong, J., et al. (2023) · Science Advances · doi:10.1126/sciadv.adf3771 · Cited by 31
Ritter, S., Zadik-Weiss, L., Almogi‐Hazan, O., & Or, R. (2020) · Rambam Maimonides Medical Journal · doi:10.5041/rmmj.10388 · Cited by 33
Luo, C., Liu, H., Xie, F.-M., et al. (2019) · bioRxiv · doi:10.1101/2019.12.11.873398 · Cited by 27
“These major populations contain intermediate neuronal populations such as PVALB-expressing Basket Cell (BC) and Chandelier Cell (ChC), or the recently reported LAMP5-expressing Rosehip neurons (Boldog et al., 2018).”
BackgroundSelf-citationGene regulatory networks during the development of the Drosophila visual system
Chen, Y., & Desplan, C. (2020) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/bs.ctdb.2020.02.010 · Cited by 28
“The nervous system is so sophisticated that even after more than one hundred years of vigorous interrogation, there are still many unknown types of neurons to be discovered (Boldog et al., 2018), which makes one wonder what underlies this enormous diversity.”
BackgroundBursting of excitatory cells is linked to interictal epileptic discharge generation in humans
Hofer, K. T., Kandrács, Á., Tóth, K., Hajnal, B., Bokodi, V., Tóth, E. Z., Erőss, L., Entz, L., Bagó, A. G., Fabó, D., et al. (2022) · Scientific Reports · doi:10.1038/s41598-022-10319-4 · Cited by 31
Functional enhancer elements drive subclass-selective expression from mouse to primate neocortexPreprint
Mich, J., Graybuck, L. T., Hess, E. E., et al. (2019) · bioRxiv · doi:10.1101/555318 · Cited by 99
“Mouse and human neocortex have a remarkable diversity of cell types (Zeisel et al., 2015; Tasic et al., 2016, 2018; Boldog et al., 2018; Hodge et al., 2019, 2020; Bakken et al., 2020).”
BackgroundSelf-citationAurelian, L., & Balan, I. S. (2019) · Psychopharmacology · doi:10.1007/s00213-019-05220-4 · Cited by 31
Early maternal care restores LINE-1 methylation and enhances neurodevelopment in preterm infants
Fontana, C., Marasca, F., Provitera, L., Mancinelli, S., Pesenti, N., Sinha, S., Passera, S., Abrignani, S., Mosca, F., Lodato, S., et al. (2021) · BMC Medicine · doi:10.1186/s12916-020-01896-0 · Cited by 29
A community-based transcriptomics classification and nomenclature of neocortical cell types
Yuste, R., Hawrylycz, M., Aalling, N., Aguilar-Valles, A., Arendt, D., Armañanzas, R., Ascoli, G. A., Bielza, C., Bokharaie, V., Bergmann, T. B., et al. (2020) · Nature Neuroscience · doi:10.1038/s41593-020-0685-8 · Cited by 32
Self-citationLourenço, J., Koukouli, F., & Bacci, A. (2020) · Cortex · doi:10.1016/j.cortex.2020.08.015 · Cited by 25
Defining the nature of human pluripotent stem cell-derived interneurons via single-cell analysis
Allison, T. F., Langerman, J., Sabri, S., Otero‐García, M., Lund, A. J., Huang, J. C., Wei, X., Samarasinghe, R. A., Polioudakis, D., Módy, I., et al. (2021) · Stem Cell Reports · doi:10.1016/j.stemcr.2021.08.006 · Cited by 24
Metadata
- Authors
- Boldog, E., Bakken, T. E., Hodge, R. D., Novotny, M., Aevermann, B. D., Baka, J., Bordé, S., Close, J. L., Diez-Fuertes, F., Ding, S.-L., Faragó, N., Kocsis, Á. K., Kovács, B., Maltzer, Z., McCorrison, J. M., Miller, J. A., Molnár, G., Oláh, G., Ozsvár, A., Rózsa, M., Shehata, S. I., Smith, K. A., Sunkin, S. M., Tran, D. N., Venepally, P., Wall, A., Puskás, L. G., Barzó, P., Steemers, F. J., Schork, N. J., Scheuermann, R. H., Lasken, R. S., Lein, E. S., & Tamás, G.
- Affiliations
- University of Szeged (HU)
- Allen Institute for Brain Science (US)
- J. Craig Venter Institute (US)
- HUN-REN Szegedi Biológiai Kutatóközpont (HU)
- Illumina (United States) (US)
- Corresponding author
- Lein, Ed S.
- Tamás, Gábor
- ORCID
- Boldog, Eszter
- Bakken, Trygve E.
- Hodge, Rebecca D.
- Novotny, Mark
- Aevermann, Brian D.
- Baka, Judith
- Bordé, Sándor
- Close, Jennie L.
- Ding, Song-Lin
- Faragó, Nóra
- Kocsis, Ágnes K.
- Kovács, Balázs
- Maltzer, Zoe
- McCorrison, Jamison M.
- Miller, Jeremy A.
- Molnár, Gábor
- Oláh, Gáspár
- Ozsvár, Attila
- Rózsa, Márton
- Shehata, Soraya I.
- Smith, Kimberly A.
- Sunkin, Susan M.
- Puskás, László G.
- Barzó, Pál
- Schork, Nicholas J.
- Scheuermann, Richard H.
- Lein, Ed S.
- Tamás, Gábor
- Venue
- Nature Neuroscience
- Published
- 2018-08-27
- Volume
- 21
- Issue
- 9
- Pages
- 1185-1195
- ISSN
- 1097-6256 (ISSN-L)
- 1546-1726
- PMC
- PMC6130849
- OpenAlex
- W2767443671
- Semantic Scholar
- 3ae2f32de897a98351ded7a44ee959ad0bc0de3d
- Cited by
- 291
- References
- 73
- Citations by year
- 2026: 21 · 2025: 29 · 2024: 28 · 2023: 58 · 2022: 27 · 2021: 31 · 2020: 44 · 2019: 43 · 2018: 10
- FWCI
- 14.57
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Neuroscience (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed (publishedVersion)
- SZTE Publicatio Repozitórium (University of Szeged) (acceptedVersion, other-oa)
- Repository of the Academy's Library (Library of the Hungarian Academy of Sciences) (acceptedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- Magyar Tudományos Akadémia
- National Institutes of Health (5u01mh114812-03)
- National Research, Development and Innovation Office (14-1-2015-0155)
- National Institute of Mental Health (U01MH114812)
- Topics
- Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Neuroscience and Neuropharmacology Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Neuroscience › Cognitive Neuroscience › Neural dynamics and brain function
- Keywords
- GABAergic interneurons, human cortex, interneuron subtypes, single-nucleus RNA sequencing, axonal boutons, dendritic branching, dendritic computation, GAD1, cholecystokinin, CNR1, parvalbumin
- MeSH terms
- Adult, Aged, Axons, Cerebral Cortex, Humans, Male, RNA, Gene Library, Polymerase Chain Reaction, Sequence Analysis, RNA, Gap Junctions, Presynaptic Terminals, Pyramidal Cells, Dendritic Spines, GABAergic Neurons, Transcriptome
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
A language model drew the claims from the paper on 2026-10-07, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-10-07 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).
Cited sources are checked with a language model’s help (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.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
