Evidence map›Paper›PMID 41882195›Full record

ArticleNature neuroscience2026

NeMO Analytics: a compendium of transcriptomic data for the exploration of neocortical development.

Shreyash Sonthalia, Brian Herb, Ricky S Adkins, Joshua Orvis, Guangyan Li, Xiangyu Liao, Qingjie Yu, Xoel Mato Blanco, Alex Casella, Jinrui Liu and 15 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature neuroscience, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

25 authors.

Shreyash SonthaliaDepartments of Neurology and Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA.
Brian HerbInstitute for Genome Sciences, University of Maryland, Baltimore, MD, USA.ORCID http://orcid.org/0000-0002-5910-9647
Ricky S AdkinsInstitute for Genome Sciences, University of Maryland, Baltimore, MD, USA.ORCID http://orcid.org/0000-0002-7983-5486
Joshua OrvisInstitute for Genome Sciences, University of Maryland, Baltimore, MD, USA.
Guangyan LiDepartments of Neurology and Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA.
Xiangyu LiaoDepartments of Neurology and Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA.
Qingjie YuDepartments of Neurology and Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA.ORCID http://orcid.org/0009-0009-3086-2713
Xoel Mato BlancoDepartment of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.
Alex CasellaInstitute for Genome Sciences, University of Maryland, Baltimore, MD, USA.ORCID http://orcid.org/0000-0001-6873-7867
Jinrui LiuDepartments of Neurology and Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA.ORCID http://orcid.org/0000-0003-0778-4701
Genevieve Stein-O'BrienDepartments of Neurology and Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA.ORCID http://orcid.org/0000-0001-8681-9110
Brian CaffoDepartment of Biostatistics, Johns Hopkins School of Public Health, Baltimore, MD, USA.
Ronna HertzanoNeurotology Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA.ORCID http://orcid.org/0000-0002-8093-6567
Anup MahurkarInstitute for Genome Sciences, University of Maryland, Baltimore, MD, USA.ORCID http://orcid.org/0000-0002-4999-2296
Jin-Chong XuDepartments of Neurology and Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA.
Jesse GillisUniversity of Toronto, Toronto, Ontario, Canada.ORCID http://orcid.org/0000-0002-0936-9774
Jonathan WernerInstitute for Genome Sciences, University of Maryland, Baltimore, MD, USA.ORCID http://orcid.org/0000-0001-9248-6420
Shaojie MaDepartment of Neuroscience, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0002-8782-3047
Suel-Kee KimDepartment of Neuroscience, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0003-0240-9304
Nicola MicaliDepartment of Neuroscience, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0009-0002-2936-4708
Nenad SestanDepartment of Neuroscience, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0003-0966-9619
Pasko RakicDepartment of Neuroscience, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0002-6963-0508
Gabriel SantpereHospital del Mar Research Institute, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain.ORCID http://orcid.org/0000-0001-5909-8637
Seth A AmentInstitute for Genome Sciences, University of Maryland, Baltimore, MD, USA.ORCID http://orcid.org/0000-0001-6443-7509
Carlo ColantuoniDepartments of Neurology and Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA. ccolantu@jhmi.edu.ORCID http://orcid.org/0000-0001-6818-6380

Funding

A Multidisciplinary Center for Developing Human and Non-human Primate Brain Cell AtlasesUM1MH130991 · NIMH · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Hao Huang, ARNOLD KRIEGSTEIN · 2022 to 2026
$25.2M
A BRAIN Initiative Resource: The Neuroscience Multi-omic Data ArchiveR24MH114788 · NIMH · UNIVERSITY OF MARYLAND BALTIMORE · PI Anup Mahurkar, Owen R White · 2017 to 2026
$17.2M
Origin of Cortical Species-specific Distinctions.R01DA023999 · NIDA · YALE UNIVERSITY · PI RAKIC, PASKO · 2008 to 2019
$7.9M
Origin of Cortical Species-specific DistinctionsR37DA023999 · NIDA · YALE UNIVERSITY · PI PASKO RAKIC · 2020 to 2026
$5.6M
Cell Type Specific Transcriptional Cascades in Inner Ear DevelopmentR01DC013817 · NIDCD · UNIVERSITY OF MARYLAND BALTIMORE · PI HERTZANO, RONNA · 2015 to 2022
$3.6M
Developmental cell census of human and non-human primate brainU01MH124619 · NIMH · YALE UNIVERSITY · PI SESTAN, NENAD · 2020 to 2022
$3.3M
Illuminating Neurodevelopment through Integrated Analysis and Vizualization of Multi-Omic DataR24MH114815 · NIMH · UNIVERSITY OF MARYLAND BALTIMORE · PI HERTZANO, RONNA, WHITE, OWEN R · 2018 to 2020
$2.3M
Identification of Genetic and Molecular Bases of Derived Phenotypes in Primate Brain DevelopmentR01HG010898 · NHGRI · YALE UNIVERSITY · PI SANTPERE BARO, GABRIEL, SESTAN, NENAD · 2020 to 2023
$2.2M
The gEAR portal - Advancing Data Sharing, Analysis and Discovery for Hearing and Balance ResearchR01DC019370 · NIDCD · UNIVERSITY OF MARYLAND BALTIMORE · PI MAHURKAR, ANUP · 2021 to 2022
$1.5M
Resolving Spatiotemporal Determinants of Cell Specification in Corticogenesis with Latent Space MethodsR00NS122085 · NINDS · JOHNS HOPKINS UNIVERSITY · PI STEIN-O'BRIEN, GENEVIEVE LAUREN · 2023 to 2025
$697k
TEMPORAL ACOUSTIC ANALYSIS IN LATERAL LEMNISCAL NUCLEIF32DC000094 · NIDCD · DUKE UNIVERSITY · PI HUFFMAN, RUSSELL F · 1992 to 1995
–
NHGRI NIH HHS R01 HG010898NIDA NIH HHS R01 DA023999NIDA NIH HHS R37 DA023999NIDCD NIH HHS F32 DC000094NIDCD NIH HHS R01 DC013817NIDCD NIH HHS R01 DC019370NIMH NIH HHS R24 MH114788NIMH NIH HHS R24 MH114815NIMH NIH HHS U01 MH124619NIMH NIH HHS UM1 MH130991NINDS NIH HHS R00 NS122085
6 · The paper itself

Abstract

Here, to enable researchers to more fully harness the collective discovery potential of multiomic data in the public domain, we have assembled gene-level transcriptomic data from ~200 studies of neocortical development and in vitro models. Applying joint matrix decomposition to mouse, macaque and human data, we define transcriptome dynamics that are conserved across neocortical neurogenesis and identify a program that emerges in ventricular progenitors, is later expressed in neurogenic outer, or basal, radial glia of primates, but is limited to gliogenic precursors in the rodent. Decomposition of adult human neocortical data identified layer-specific signatures in excitatory neurons, enabling the charting of their developmental emergence and protracted maturation, which is in stark contrast to the early peaking expression of layer-defining transcription factors. Interrogation of data from cerebral organoids demonstrated that, although broad elements of in vivo development are recapitulated in vitro, many layer-specific transcriptomic programs in neuronal maturation are absent. We invite cell biologists without coding expertise to use NeMO Analytics in their research and to fuel it with their own emerging data at nemoanalytics.org/landing/neocortex .

Indexed as

NeocortexNeurogenesisTranscriptomeAnimalsGene Expression Regulation, DevelopmentalHumansMacacaMiceNeurodevelopmentNeurons

Identifiers

PMID41882195
PMCPMC13061640

What OpenQuestion holds

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LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.