Cited by 1,065Single-cell and spatial transcriptomicsNeuroscience and Neuropharmacology ResearchMemory and Neural Mechanisms

The DOI matches its Crossref record; 88 of the 88 references it cites were found in a registry or an index; none of the 65 sources its claims cite is checked for support yet.

A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation

Open access

Yao, Zizhen, van Velthoven, Cindy T.J., Nguyen, Thuc Nghi, Goldy, Jeff, Sedeno-Cortes, Adriana E., Baftizadeh, Fahimeh, Bertagnolli, Darren, Casper, Tamara, Chiang, Megan, Crichton, Kirsten, Ding, Song-Lin, Fong, Olivia, Garren, Emma, Glandon, Alexandra, Gouwens, Nathan W., Gray, James, Graybuck, Lucas T., Hawrylycz, Michael J., Hirschstein, Daniel, Kroll, Matthew, Lathia, Kanan, Lee, Changkyu, Levi, Boaz, McMillen, Delissa, Mok, Stephanie, Pham, Thanh, Ren, Qingzhong, Rimorin, Christine, Shapovalova, Nadiya, Sulc, Josef, Sunkin, Susan M., Tieu, Michael, Torkelson, Amy, Tung, Herman, Ward, Katelyn, Dee, Nick, Smith, Kimberly A., Tasic, Bosiljka, Zeng, Hongkui·2021·Cell

DOI 10.1016/j.cell.2021.04.021PMC PMC8195859

Published version of a preprint

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Abstract

SUMMARY The isocortex and hippocampal formation (HPF) in the mammalian brain play critical roles in perception, cognition, emotion and learning. We profiled ~1.3 million cells covering the entire adult mouse isocortex and HPF and derived a transcriptomic cell type taxonomy revealing a comprehensive repertoire of glutamatergic and GABAergic neuron types. Contrary to the traditional view of HPF as having a simpler cellular organization, we discover a complete set of glutamatergic types in HPF homologous to all major subclasses found in the six-layered isocortex, suggesting that HPF and isocortex share a common circuit organization. We also identify large-scale continuous and graded variation of cell types along isocortical depth, across isocortical sheet and in multiple dimensions in hippocampus and subiculum. Overall, our study establishes a molecular architecture of mammalian isocortex and hippocampal formation and begins to shed light on its underlying relationship with the development, evolution, connectivity and function of these brain structures.

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Crossref · 10.1016/j.cell.2021.04.021

Cites

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Claims the paper makes

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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 GABAergic inhibitory neuronal class is divided into two neighborhoods that correlate with distinct developmental origins: caudal ganglionic eminence (CGE) (Fig. 2A–E) and medial ganglionic eminence (MGE) (Fig. 2F–J).”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > RESULTS > GABAergic cell type taxonomy
Load-bearingStrength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
- Rests on an assumption: Transcriptomic neighborhoods of GABAergic neurons correlate with distinct developmental origins (CGE and MGE).
In the paper
“Our CTX-HPF GABAergic taxonomy corresponds well with a previous scRNA-seq study of CA1 interneurons (Harris et al., 2018), particularly for some HPF-specific clusters identified here”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > RESULTS > GABAergic cell type taxonomy
What the sources say
- Not checked yetcites Harris et al., 2018 source
Strength:boosted· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
None of the sources cited for this claim have been checked yet.
In the paper
“Comparing this taxonomy with six previous studies (Cembrowski et al., 2018; Harris et al., 2018; Saunders et al., 2018; Tasic et al., 2018; Yao et al., 2020; Zeisel et al., 2018), we found generally good but variable correspondences”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > RESULTS > Generation of the transcriptomic cell type taxonomy
What the sources say
- Not checked yetcites Cembrowski et al., 2018 source
- Not checked yetcites Harris et al., 2018 source
- Not checked yetcites Saunders et al., 2018 source
Strength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
In the paper
“the most dorsal clusters in CA1, CA3 and SUB show high levels of activity-dependent gene expression compared to the ventral part”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > RESULTS > Multidimensional variation of cell type distribution in the hippocampal and subicular regions
What the sources say
- Not checked yetcites Chawla et al., 2018 source
Strength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
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 approach revealed that most HPF cell types match a specific CTX subclass.”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > RESULTS > Glutamatergic cell type taxonomy
Load-bearingStrength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
- Rests on an assumption: Correlation of gene expression between HPF and CTX clusters indicates homology.
In the paper
“We did not find clusters strongly related to adult neurogenesis in DG (Goncalves et al., 2016)”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > RESULTS > Multidimensional variation of cell type distribution in the hippocampal and subicular regions
What the sources say
- Not checked yetcites Goncalves et al., 2016 source
Strength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
In the paper
“The L2/3 RHP subclass contains two supertypes assigned to the superficial layers of ProS (L2/3 IT ProS Dcn Cbln4, Fig. 4I–J) and HATA (IT HATA Id4, also extending to ventral ENT) regions (Ding et al., 2020).”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > RESULTS > Comparison of glutamatergic cell types between hippocampal formation and isocortex
What the sources say
- Not checked yetcites Ding et al., 2020 source
Strength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
In the paper
“In the CA3 subclass, we identify a hilar mossy cell supertype, Mossy Rgs12, based on multiple marker genes including Gal, Rgs12, Glipr1, Necab1 and Calb2 (Scharfman and Myers, 2012)”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > RESULTS > Multidimensional variation of cell type distribution in the hippocampal and subicular regions
What the sources say
- Not checked yetcites Scharfman and Myers, 2012
Strength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
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
“Many markers expressed at the superficial layer such as Dio3 in the middle section of the Ve-Do axis have ubiquitous expression in the ventral CA1, positioning the ventral CA1 closer to the superficial end of the pseudo Su-De axis”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > STAR METHODS > METHOD DETAILS
Load-bearingStrength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
- Rests on an assumption: The top principal component computed from a selected gene set faithfully represents the biological axis it is named after (e.g., Pr-Di, Do-Ve, Su-De, activity).
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 UMAP for each subclass revealed much clearer regional diversities.”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > STAR METHODS > METHOD DETAILS
Strength:boosted· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
- Rests on an assumption: The top principal component computed from a selected gene set faithfully represents the biological axis it is named after (e.g., Pr-Di, Do-Ve, Su-De, activity).
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
“UMAP instead of PCA was chosen here as we observed a nonlinear relationship.”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > STAR METHODS > METHOD DETAILS
Load-bearingStrength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
- Rests on an assumption: The top principal component computed from a selected gene set faithfully represents the biological axis it is named after (e.g., Pr-Di, Do-Ve, Su-De, activity).
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 the PCA space, L6 IT types were more similar to L2/3 IT types than L5 IT types to L2/3 IT types.”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > STAR METHODS > METHOD DETAILS
Strength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
- Rests on an assumption: The top principal component computed from a selected gene set faithfully represents the biological axis it is named after (e.g., Pr-Di, Do-Ve, Su-De, activity).
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 top PC based on this set of genes is defined as the CA3 Pr-Di axis, which also correlates heavily with the Do-Ve axis.”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > STAR METHODS > METHOD DETAILS
Strength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
- Rests on an assumption: The top principal component computed from a selected gene set faithfully represents the biological axis it is named after (e.g., Pr-Di, Do-Ve, Su-De, activity).
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 medial (RSP/ACA) and lateral (AI/TPE) regions were highly distinct”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > STAR METHODS > METHOD DETAILS
Strength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
- Rests on an assumption: The top principal component computed from a selected gene set faithfully represents the biological axis it is named after (e.g., Pr-Di, Do-Ve, Su-De, activity).
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
“there were clear transitions between adjacent layers, which were preserved faithfully, by one dimensional UMAP.”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > STAR METHODS > METHOD DETAILS
Load-bearingStrength:boosted· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
- Rests on an assumption: The top principal component computed from a selected gene set faithfully represents the biological axis it is named after (e.g., Pr-Di, Do-Ve, Su-De, activity).
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
“anterior-posterior gradient could be observed in almost all cases.”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > STAR METHODS > METHOD DETAILS
Strength:hedged· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
- Rests on an assumption: The top principal component computed from a selected gene set faithfully represents the biological axis it is named after (e.g., Pr-Di, Do-Ve, Su-De, activity).
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 computed one dimensional UMAP for all the IT cells based on the PCs in the imputed space (see section UMAP projection), which corresponded very well with cortical depth.”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > STAR METHODS > METHOD DETAILS
Strength:boosted· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
- Rests on an assumption: The top principal component computed from a selected gene set faithfully represents the biological axis it is named after (e.g., Pr-Di, Do-Ve, Su-De, activity).
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“our study establishes a molecular architecture of mammalian isocortex and hippocampal formation”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > Abstract
Load-bearingStrength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
- Rests on an assumption: Mouse isocortex and hippocampal formation are representative of mammalian isocortex and hippocampal formation.
None of the sources cited for this claim have been checked yet.
In the paper
“Isocortical and hippocampal GABAergic interneuron types are similarly organized by their embryonic origins, firing characteristics and local connectivity patterns”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > INTRODUCTION
What the sources say
- Not checked yetcites Fishell and Rudy, 2011 source
- Not checked yetcites Pelkey et al., 2017 source
- Not checked yetcites Tremblay et al., 2016 source
Load-bearingStrength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
None of the sources cited for this claim have been checked yet.
In the paper
“These studies demonstrate the validity and power of using the highly scalable scRNA-seq approach to generate a comprehensive census of cell types as a foundation for further structural and functional studies of brain circuits.”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > INTRODUCTION
What the sources say
- Not checked yetcites Gouwens et al., 2020 source
- Not checked yetcites Scala et al., 2020
- Not checked yetcites Tasic et al., 2018 source
Load-bearingStrength:boosted· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
In the paper
“is likely derived from MGE instead of CGE (Pelkey et al., 2017)”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > RESULTS > GABAergic cell type taxonomy
What the sources say
- Not checked yetcites Pelkey et al., 2017 source
Strength:hedged· not yet calibratedCausal:conditional· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
In the paper
“The Cxcr4+ cells may correspond to the hilar performant path-associated (HIPP) or DG somatostatin-expressing-interneurons (DG-SOMIs) described previously (Yuan et al., 2017).”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > RESULTS > GABAergic cell type taxonomy
What the sources say
- Not checked yetcites Yuan et al., 2017 source
Strength:hedged· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
In the paper
“using the Patch-seq approach, we simultaneously profiled the transcriptomic, electrophysiological, and morphological properties of a large set of GABAergic interneurons from mouse visual cortex and found excellent correspondence among the three modalities”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > INTRODUCTION
What the sources say
- Not checked yetcites Gouwens et al., 2020 source
Load-bearingStrength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
In the paper
“This supertype likely represents the L4 spiny stellate or star pyramid neurons that are morphologically distinct from the pyramidal neurons in other layers (Harris and Shepherd, 2015)”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > RESULTS > Continuous variation of glutamatergic neuron types across layers and regions of isocortex
What the sources say
- Not checked yetcites Harris and Shepherd, 2015 source
Strength:hedged· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
In the paper
“CA1, CA3 and SUB have gradual gene expression and connectivity changes along multiple dimensions – superficial-deep, proximal-distal and dorsal-ventral (Cembrowski and Spruston, 2019).”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > RESULTS > Multidimensional variation of cell type distribution in the hippocampal and subicular regions
What the sources say
- Not checked yetcites Cembrowski and Spruston, 2019 source
Strength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
In the paper
“suggesting ProS contains cell types similar to either SUB or CA1, as in our previous study (Ding et al., 2020)”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > RESULTS > Glutamatergic cell type taxonomy
What the sources say
- Not checked yetcites Ding et al., 2020 source
Strength:hedged· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“we also provided an estimate of the relative proportions of different cell types in each region using the 10xv2 data”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > DISCUSSION > Limitations of the Study
Strength:hedged· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
- Rests on an assumption: The relative proportions estimated from 10xv2 data reflect true proportions of cell types in each region.
None of the sources cited for this claim have been checked yet.
In the paper
“This finding challenges the traditional view that isocortex is newly evolved whereas HPF remains as an older structure during vertebrate evolution”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > DISCUSSION
What the sources say
- Not checked yetcites Northcutt and Kaas, 1995 source
- Not checked yetcites Tosches and Laurent, 2019 source
Load-bearingStrength:plain· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
In the paper
“This difference in developmental origins may be the underlying reason for the dichotomy between the extensive regional diversity of glutamatergic types and the sharing of a common set of GABAergic types across isocortical regions”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > DISCUSSION
What the sources say
- Not checked yetcites Tasic et al., 2018 source
Strength:hedged· not yet calibratedCausal:conditional· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“we assigned anatomical locations of major cell types (mostly at the supertype level) using existing RNA ISH data from the Allen Mouse Brain Atlas and a limited Visium dataset”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > DISCUSSION > Limitations of the Study
Load-bearingStrength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
- Rests on an assumption: The anatomical locations assigned using existing RNA ISH data from the Allen Mouse Brain Atlas and a limited Visium dataset are accurate enough for major cell types.
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
“Nevertheless, the relative positions along pseudo Su-De axis for ventral and dorsal clusters still make sense.”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > STAR METHODS > METHOD DETAILS
Strength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
- Rests on an assumption: The top principal component computed from a selected gene set faithfully represents the biological axis it is named after (e.g., Pr-Di, Do-Ve, Su-De, activity).
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This is a very conservative estimate of regional specificity, as it is possible that we might have missed the specificity contributed by very small sets of genes.”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > STAR METHODS > METHOD DETAILS
Strength:hedged· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
- Rests on an assumption: The 10xv2 and SSv4 datasets share conserved global transcriptional signatures that permit cross-platform mapping of regional identity.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Therefore, the pseudo Su-De axis is confounded with the Ve-Do axis.”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > STAR METHODS > METHOD DETAILS
Load-bearingStrength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
- Rests on an assumption: The top principal component computed from a selected gene set faithfully represents the biological axis it is named after (e.g., Pr-Di, Do-Ve, Su-De, activity).
In the paper
“This is consistent with the previously defined CA3 subdomains (Thompson et al., 2008), which divided CA3 into a series of diagonal bands oriented septal-distally (toward CA2) to temporal-proximally (toward DG).”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > STAR METHODS > METHOD DETAILS
What the sources say
- Not checked yetcites Thompson et al., 2008 source
Strength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
- Rests on an assumption: The top principal component computed from a selected gene set faithfully represents the biological axis it is named after (e.g., Pr-Di, Do-Ve, Su-De, activity).

It may state two separate claims as one. 123
Probably not a substantial claim. 43
The quote only partly states this claim. 1

None of the sources cited for this claim have been checked yet.
In the paper
“For CGE, the Ntng1 HPF supertype does not express canonical pan-CGE marker Prox1 (Miyoshi et al., 2015; Rubin and Kessaris, 2013) nor its subclass markers Vip, Sncg or Lamp5”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > RESULTS > GABAergic cell type taxonomy
What the sources say
- Not checked yetcites Miyoshi et al., 2015 source
- Not checked yetcites Rubin and Kessaris, 2013
Load-bearingStrength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
It may state two separate claims as one.
In the paper
“most clusters are shared by all isocortical areas, consistent with our previous observations (Tasic et al., 2018), and also by RHP regions”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > RESULTS > GABAergic cell type taxonomy
What the sources say
- Not checked yetcites Tasic et al., 2018 source
Load-bearingStrength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“It is also consistent with the large body of literature on cortical GABAergic interneurons (Lim et al., 2018; Pelkey et al., 2017; Tremblay et al., 2016), and our Patch-seq study (Gouwens et al., 2020) with MET types defined in that study corresponding well with the supertypes defined here”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > RESULTS > GABAergic cell type taxonomy
What the sources say
- Not checked yetcites Lim et al., 2018 source
- Not checked yetcites Pelkey et al., 2017 source
- Not checked yetcites Tremblay et al., 2016 source
Strength:boosted· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“The current CTX-HPF GABAergic taxonomy is largely consistent with previous transcriptomic taxonomies derived from cortical areas VISp-ALM (Tasic et al., 2018) and MOp (Yao et al., 2020) at the supertype level but exhibits notable ambiguity at the type/cluster level”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > RESULTS > GABAergic cell type taxonomy
What the sources say
- Not checked yetcites Tasic et al., 2018 source
- Not checked yetcites Yao et al., 2020
Load-bearingStrength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
It may state two separate claims as one.
In the paper
“Projection mapping (http://connectivity.brain-map.org/; experiments 166269090, 166458363 and 181860879) (Oh et al., 2014) showed that neurons labeled via Scnn1a-Tg3-Cre driver line in RSP have long-range projections to both intra- and extratelencephalic targets; they project to ACA, RHP regions, contralateral RSP, and anteroventral nucleus (AV) of thalamus”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > RESULTS > Comparison of glutamatergic cell types between hippocampal formation and isocortex
What the sources say
- Not checked yetcites Oh et al., 2014
Load-bearingStrength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“The three ALM L5 PT types previously identified (Economo et al., 2018; Tasic et al., 2018) correspond to cluster #248 (thalamus-projecting cells) in the Npnt supertype and clusters #249 and #252 (medulla-projecting cells) in the Cdh13 supertype, respectively”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > RESULTS > Comparison of glutamatergic cell types between hippocampal formation and isocortex
What the sources say
- Not checked yetcites Economo et al., 2018 source
- Not checked yetcites Tasic et al., 2018 source
Load-bearingStrength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
It may state two separate claims as one.
In the paper
“Across all isocortical areas, most glutamatergic cell types are shared among multiple areas (Fig. 3B, S2), contrary to what we found in our previous study of two distantly located cortical areas, VISp and ALM”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > DISCUSSION
What the sources say
- Not checked yetcites Tasic et al., 2018 source
Load-bearingStrength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
It may state two separate claims as one.
In the paper
“a previously known CA3 proximal gene, Fmo1 (Thompson et al., 2008), that is expressed in dorsal clusters #356 and #358, but not #357.”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > STAR METHODS > METHOD DETAILS
What the sources say
- Not checked yetcites Thompson et al., 2008 source
Load-bearingStrength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“while many deep layer markers such as Lpl have ubiquitous expression in the dorsal distal CA1, positioning these cells closer to the deep end of the pseudo Su-De axis.”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > STAR METHODS > METHOD DETAILS
Load-bearingStrength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
It may state two separate claims as one.
- Rests on an assumption: The top principal component computed from a selected gene set faithfully represents the biological axis it is named after (e.g., Pr-Di, Do-Ve, Su-De, activity).
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
“While our initial attempt using random forest classifier produced a very strong result (data not shown), we realized that the results were partially driven by donor-specific genes.”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > STAR METHODS > METHOD DETAILS
Load-bearingStrength:plain· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
It may state two separate claims as one.
- Rests on an assumption: Donor-specific transcriptional signatures are subtle and do not affect the global clustering results.
In the paper
“Glutamatergic neuronal types are organized by layers and their long-range projection patterns”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > INTRODUCTION
What the sources say
- Not checked yetcites Harris and Shepherd, 2015 source
Strength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“Archicortex and paleocortex are considered evolutionarily older structures, whereas iso/neocortex emerged later and substantially expanded in vertebrate evolution”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > INTRODUCTION
What the sources say
- Not checked yetcites Rakic, 2009 source
Strength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“their tremendous diversity in interareal axon-projection patterns forms the structural basis of the hierarchical network”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > INTRODUCTION
What the sources say
- Not checked yetcites D’Souza et al., 2016 source
- Not checked yetcites Harris et al., 2019 source
Strength:plain· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“This area specialization is likely a major contributing factor to the diversity of functions supported by cortex”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > INTRODUCTION
What the sources say
- Not checked yetcites Cadwell et al., 2019 source
Strength:hedged· not yet calibratedCausal:conditional· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
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 cortex is partitioned into multiple areas with specific input and output connections with many subcortical and other cortical regions”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > INTRODUCTION
What the sources say
- Not checked yetcites Rakic, 2009 source
- Not checked yetcites Van Essen and Glasser, 2018
Strength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“Developmentally, cortex originates from pallium, a main part of the telencephalon, which can be divided into several parts”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > INTRODUCTION
What the sources say
- Not checked yetcites Pessoa et al., 2019 source
Strength:plain· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
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
“Many molecular, anatomical, and physiological studies have revealed a broad spectrum of neuronal cell types in different cortical and hippocampal regions”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > INTRODUCTION
What the sources say
- Not checked yetcites Zeng and Sanes, 2017 source
Strength:boosted· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
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
“these neocortical areas together form a hierarchical neural network with functionally distinct modules and feedforward and feedback pathways both within and between modules”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > INTRODUCTION
What the sources say
- Not checked yetcites Coogan and Burkhalter, 1993
- Not checked yetcites Felleman and Van Essen, 1991 source
- Not checked yetcites Harris et al., 2019 source
Strength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
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
“there is a prominent functional transition along the dorsal-ventral axis of HPF, with the dorsal network mainly mediating spatial navigation and the ventral network mainly mediating emotional behaviors”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > INTRODUCTION
What the sources say
- Not checked yetcites Cembrowski and Spruston, 2019
Strength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Since isocortical Sst Myh8 and Etv1 cells are L5 Martinotti cells (Gouwens et al., 2020) (Fig. S1B), the HPF Myh8 and Etv1 cells are likely the Martinotti-like oriens lacunosum-moleculare (OLM) cells (Leao et al., 2012).”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > RESULTS > GABAergic cell type taxonomy
What the sources say
- Not checked yetcites Gouwens et al., 2020 source
- Not checked yetcites Leao et al., 2012 source
Load-bearingStrength:hedged· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
It may state two separate claims as one.
In the paper
“Previously, we analyzed single-cell transcriptomes to define 133 cell types in two isocortical areas, primary visual cortex (VISp) and anterolateral motor cortex (ALM), in mice (Tasic et al., 2018) and found that they have shared GABAergic interneuron types but distinct glutamatergic neuron types.”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > INTRODUCTION
What the sources say
- Not checked yetcites Tasic et al., 2018 source
Strength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
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
“Note that some of the CGE cell types (e.g., some neurogliaform cells) may, in fact, be developmentally derived from the nearby preoptic region (PO) (Niquille et al., 2018).”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > RESULTS > GABAergic cell type taxonomy
What the sources say
- Not checked yetcites Niquille et al., 2018 source
Strength:hedged· not yet calibratedCausal:conditional· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“Meis2 neurons were identified as related to olfactory bulb interneurons (Frazer et al., 2017).”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > RESULTS > Generation of the transcriptomic cell type taxonomy
What the sources say
- Not checked yetcites Frazer et al., 2017 source
Strength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“The distinct subclass of Car3, which includes neurons from L6 of many lateral cortical areas, is included here as our previous study showed that these Car3+ L6 neurons, like cortical IT neurons, have extensive intracortical axon projections (Peng et al., 2020).”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > RESULTS > Glutamatergic cell type taxonomy
What the sources say
- Not checked yetcites Peng et al., 2020
Strength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Single-cell RNA-sequencing (scRNA-seq) studies have systematically characterized and classified cell types in individual regions of isocortex and hippocampus”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > INTRODUCTION
What the sources say
- Not checked yetcites Harris et al., 2018 source
- Not checked yetcites Hodge et al., 2019 source
- Not checked yetcites Tasic et al., 2016 source
Load-bearingStrength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
Probably not a substantial claim.
In the paper
“likely corresponds to a subset of cortical L2/3 neurons that express IEG c-fos under basal conditions and are preferentially interconnected within the L2/3 network (Yassin et al., 2010)”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > RESULTS > Continuous variation of glutamatergic neuron types across layers and regions of isocortex
What the sources say
- Not checked yetcites Yassin et al., 2010 source
Strength:hedged· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“This prediction is highly consistent with the currently known interareal connections of HPF, providing a level of validation to the transcriptomic cell type framework”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > DISCUSSION
What the sources say
- Not checked yetcites Bienkowski et al., 2018 source
- Not checked yetcites Ding et al., 2020 source
- Not checked yetcites Gergues et al., 2020 source
Load-bearingStrength:boosted· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
It may state two separate claims as one.
In the paper
“In addition to the classical single-cell clustering processing steps provided by other tools such as Seurat (Butler et al., 2018), this package features automatic iterative clustering while ensuring all pairs of clusters, even at the finest level, are separable by fairly stringent differential gene expression criteria (Tasic et al., 2018).”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > STAR METHODS > METHOD DETAILS
What the sources say
- Not checked yetcites Tasic et al., 2018 source
Strength:plain· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
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
“The combination of these region-specific cell types and the continuous variation of shared cell types across isocortical areas collectively defines cortical areal modularity”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > DISCUSSION
What the sources say
- Not checked yetcites Harris et al., 2019 source
Load-bearingStrength:plain· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Therefore, the prediction was based on global transcription signatures that are conserved across platforms, with no particular genes heavily weighted.”
§ A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation > STAR METHODS > METHOD DETAILS
Load-bearingStrength:plain· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
It may state two separate claims as one.
- Rests on an assumption: The 10xv2 and SSv4 datasets share conserved global transcriptional signatures that permit cross-platform mapping of regional identity.

142 of 142

The authors state this as an assumption.
A systematic study is needed for a complete picture of the number and distribution of cell types in isocortex and HPF and for understanding how these regions interact with the rest of the brain.
“But a systematic study is needed for a complete picture of the number and distribution of cell types in these regions and for understanding how different cortical and hippocampal regions interact with the rest of the brain and carry out their individual functions.”
The paper relies on this without support.
Fewer differentially expressed genes between two clusters indicates greater relatedness or similarity.
“the fewer DE genes, the more related”
The paper relies on this without support.
Correlation of gene expression between HPF and CTX clusters indicates homology.
“correlating gene expression for each HPF cell to the average expression of each CTX cluster”
The paper relies on this without support.
Mouse isocortex and hippocampal formation are representative of mammalian isocortex and hippocampal formation.
“our study establishes a molecular architecture of mammalian isocortex and hippocampal formation”
The paper relies on this without support.
Transcriptomic neighborhoods of GABAergic neurons correlate with distinct developmental origins (CGE and MGE).
“The GABAergic inhibitory neuronal class is divided into two neighborhoods that correlate with distinct developmental origins: caudal ganglionic eminence (CGE) (Fig. 2A–E) and medial ganglionic eminence (MGE) (Fig. 2F–J).”
The paper relies on this without support.
The anatomical locations assigned using existing RNA ISH data from the Allen Mouse Brain Atlas and a limited Visium dataset are accurate enough for major cell types.
“we assigned anatomical locations of major cell types (mostly at the supertype level) using existing RNA ISH data from the Allen Mouse Brain Atlas and a limited Visium dataset”
The paper relies on this without support.
The relative proportions estimated from 10xv2 data reflect true proportions of cell types in each region.
“we also provided an estimate of the relative proportions of different cell types in each region using the 10xv2 data”
The paper relies on this without support.
The top principal component computed from a selected gene set faithfully represents the biological axis it is named after (e.g., Pr-Di, Do-Ve, Su-De, activity).
“The top PC based on this set of genes is defined as the CA3 Pr-Di axis”
“defined the pseudo superficial-deep (Su-De) axis as the top PC based on these layer-specific genes”
“computed the top PC based on this gene set as the activity axis”
The paper relies on this without support.
The 10xv2 and SSv4 datasets share conserved global transcriptional signatures that permit cross-platform mapping of regional identity.
“the prediction was based on global transcription signatures that are conserved across platforms”
The paper relies on this without support.
Donor-specific transcriptional signatures are subtle and do not affect the global clustering results.
“While donor-specific transcriptional signatures are subtle and do not affect the global clustering results”

10 of 10

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?

Self-check

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

Class-level subclass counts omit two subclasses
Minor
The four class counts of 6, 28, 2, and 4 subclasses sum to 40 rather than 42. CR and Meis2 are subsequently identified as neuronal subclasses, but are not accounted for in the stated class breakdown.
Reported 42 · recomputed 40

1 of 1

STAR: ultrafast universal RNA-seq aligner
Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709
Comprehensive Integration of Single-Cell Data
Stuart, T., Butler, A., Hoffman, P., Hafemeister, C., Papalexi, E., Mauck, W. M., Hao, Y., Stoeckius, M., Smibert, P., & Satija, R. (2019) · Cell · doi:10.1016/j.cell.2019.05.031 · Cited by 15,453
Integrating single-cell transcriptomic data across different conditions, technologies, and species
Butler, A., Hoffman, P., Smibert, P., Papalexi, E., & Satija, R. (2018) · Nature Biotechnology · doi:10.1038/nbt.4096 · Cited by 13,174
UMAP: Uniform Manifold Approximation and Projection
McInnes, L., Healy, J., Saul, N., & Großberger, L. (2018) · Journal of Open Source Software · doi:10.21105/joss.00861 · Cited by 9,826
Distributed hierarchical processing in the primate cerebral cortex
Felleman, D. J., & Van Essen, D. C. (1991) · Cerebral Cortex · doi:10.1093/cercor/1.1.1 · Cited by 7,783
A robust and high-throughput Cre reporting and characterization system for the whole mouse brain
Madisen, L., Zwingman, T. A., Sunkin, S. M., Oh, S. W., Zariwala, H. A., Gu, H., Ng, L. L., Palmiter, R. D., Hawrylycz, M. J., Jones, A. R., et al. (2010) · Nature Neuroscience · doi:10.1038/nn.2467 · Cited by 6,907
Self-citation
Genome-wide atlas of gene expression in the adult mouse brain
Lein, E. S., Hawrylycz, M. J., Ao, N., Ayres, M., Bensinger, A., Bernard, A., Boe, A. F., Boguski, M. S., Brockway, K. S., Byrnes, E. J., et al. (2007) · Nature · doi:10.1038/nature05453 · Cited by 5,572
Self-citation
DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors
McGinnis, C. S., Murrow, L. M., & Gartner, Z. J. (2019) · Cell Systems · doi:10.1016/j.cels.2019.03.003 · Cited by 4,521
Software for Computing and Annotating Genomic Ranges
Lawrence, M. F., Huber, W. K., Pagès, H., Aboyoun, P., Carlson, M. R. J., Gentleman, R. C., Morgan, M. T., & Carey, V. J. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003118 · Cited by 4,475
Preface: Cerebral Cortex Has Come of Age
Goldman, P. S., & RAKIC, P. T. (1991) · Cerebral Cortex · doi:10.1093/cercor/1.1.1-a · Cited by 3,537

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Cell2location maps fine-grained cell types in spatial transcriptomics
Kleshchevnikov, V., Shmatko, A., Dann, E., Aivazidis, A., King, H. W., Li, T., Elmentaite, R., Lomakin, A., Kedlian, V., Gayoso, A., et al. (2022) · Nature Biotechnology · doi:10.1038/s41587-021-01139-4 · Cited by 1,279
A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain
Yao, Z., van Velthoven, C. T. J., Kunst, M., Zhang, M., McMillen, D., Lee, C., Jung, W., Goldy, J., Abdelhak, A., Aitken, M., et al. (2023) · Nature · doi:10.1038/s41586-023-06812-z · Cited by 1,203
Self-citation
A multimodal cell census and atlas of the mammalian primary motor cortex
BRAIN Initiative Cell Census Network (BICCN), BRAIN Initiative Cell Census Network (BICCN) Corresponding authors, Callaway, E. M., Dong, H.-W., Ecker, J. R., Hawrylycz, M. J., Huang, Z. J., Lein, E. S., Ngai, J., Osten, P., et al. (2021) · Nature · doi:10.1038/s41586-021-03950-0 · Cited by 522
Self-citation
Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells
Gouwens, N. W., Sorensen, S. A., Baftizadeh, F., Budzillo, A., Lee, B. R., Jarsky, T., Alfiler, L., Baker, K., Barkan, E., Berry, K., et al. (2020) · Cell · doi:10.1016/j.cell.2020.09.057 · Cited by 538
Self-citation
Spatially resolved cell atlas of the mouse primary motor cortex by MERFISH
Zhang, M., Eichhorn, S. W., Zingg, B., Yao, Z., Cotter, K., Zeng, H., Dong, H., & Zhuang, X. (2021) · Nature · doi:10.1038/s41586-021-03705-x · Cited by 498
Self-citation

See all 1,065

Authors: Yao, Z., van Velthoven, C. T. J., Nguyen, T. N., Goldy, J., Sedeno-Cortes, A. E., Baftizadeh, F., Bertagnolli, D., Casper, T., Chiang, M., Crichton, K., Ding, S.-L., Fong, O., Garren, E., Glandon, A., Gouwens, N. W., Gray, J., Graybuck, L. T., Hawrylycz, M. J., Hirschstein, D., Kroll, M., Lathia, K., Lee, C., Levi, B., McMillen, D., Mok, S., Pham, T., Ren, Q., Rimorin, C., Shapovalova, N., Sulc, J., Sunkin, S. M., Tieu, M., Torkelson, A., Tung, H., Ward, K., Dee, N., Smith, K. A., Tasic, B., & Zeng, H.
Affiliations: Allen Institute for Brain Science (US)
Corresponding author: Zeng, Hongkui
ORCID: Yao, Zizhen
Nguyen, Thuc Nghi
Goldy, Jeff
Baftizadeh, Fahimeh
Bertagnolli, Darren
Casper, Tamara
Chiang, Megan
Crichton, Kirsten
Ding, Song-Lin
Fong, Olivia
Glandon, Alexandra
Gouwens, Nathan W.
Graybuck, Lucas T.
Hawrylycz, Michael J.
Hirschstein, Daniel
Kroll, Matthew
Lathia, Kanan
Lee, Changkyu
Levi, Boaz
McMillen, Delissa
Mok, Stephanie
Ren, Qingzhong
Rimorin, Christine
Shapovalova, Nadiya
Sunkin, Susan M.
Tieu, Michael
Torkelson, Amy
Tung, Herman
Ward, Katelyn
Dee, Nick
Smith, Kimberly A.
Tasic, Bosiljka
Zeng, Hongkui
Venue: Cell
Publisher: Elsevier BV
Published: 2021-06
Volume: 184
Issue: 12
Pages: 3222-3241.e26
ISSN: 0092-8674 (ISSN-L)
DOI: 10.1016/j.cell.2021.04.021
PMC: PMC8195859
OpenAlex: W3162218953
Semantic Scholar: c60f04ef990c1f8b8d4c22e7ace44a70cc4bca3f
Cited by: 1,065
References: 85
Citations by year: 2026: 189 · 2025: 223 · 2024: 243 · 2023: 186 · 2022: 122 · 2021: 83
FWCI: 50.70
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/legal/tdmrep-license (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 374 d)
doi.org/10.15223/policy-017 (stm-asf)
doi.org/10.15223/policy-037 (stm-asf)
doi.org/10.15223/policy-012 (stm-asf)
doi.org/10.15223/policy-029 (stm-asf)
doi.org/10.15223/policy-004 (stm-asf)
Locations: Cell (publishedVersion)
bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
SSRN Electronic Journal (acceptedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
Funders: National Institutes of Health
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Neuroscience and Neuropharmacology Research
Life Sciences › Neuroscience › Cognitive Neuroscience › Memory and Neural Mechanisms
Keywords: neocortex, hippocampal formation, glutamatergic neurons, GABAergic neurons, neuronal cell types, subiculum, mouse brain, single-cell transcriptomics
MeSH terms: Animals, Hippocampus, Mice, Inbred C57BL, Mice, Transgenic, Glutamic Acid, Neocortex, Mice, GABAergic Neurons, Transcriptome

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A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation

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