Evidence map›Paper›PMID 38464021›Full record

ArticlebioRxiv : the preprint server for biology2024

A Curated Compendium of Transcriptomic Data for the Exploration of Neocortical Development.

Shreyash Sonthalia, Ricky S Adkins, Joshua Orvis, Guangyan Li, Xoel Mato Blanco, Alex Casella, Jinrui Liu, Genevieve Stein-O'Brien, Brian Caffo, Ronna Hertzano and 10 more

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

0 citing papers in PubMed, 4 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

20 authors at 7 institutions in 3 countries.

Shreyash SonthaliaDepts. of Neurology and Neuroscience Johns Hopkins School of Medicine, Baltimore, MD, USA.
Ricky S AdkinsUniversity of Maryland, Institute for Genome Sciences, Baltimore, MD, USA.
Joshua OrvisUniversity of Maryland, Institute for Genome Sciences, Baltimore, MD, USA.
Guangyan LiDepts. of Neurology and Neuroscience Johns Hopkins School of Medicine, Baltimore, MD, USA.
Xoel Mato BlancoDepartment of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.ORCID 0000-0003-2155-9922
Alex CasellaUniversity of Maryland, Institute for Genome Sciences, Baltimore, MD, USA.
Jinrui LiuDepts. of Neurology and Neuroscience Johns Hopkins School of Medicine, Baltimore, MD, USA.
Genevieve Stein-O'BrienDepts. of Neurology and Neuroscience Johns Hopkins School of Medicine, Baltimore, MD, USA.
Brian CaffoDept. 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.
Anup MahurkarUniversity of Maryland, Institute for Genome Sciences, Baltimore, MD, USA.
Jesse GillisUniversity of Toronto, Toronto, Canada.
Jonathan WernerUniversity of Toronto, Toronto, Canada.
Shaojie MaDepartment of Neuroscience, Yale University, New Haven CT, USA.
Nicola MicaliDepartment of Neuroscience, Yale University, New Haven CT, USA.
Nenad SestanDepartment of Neuroscience, Yale University, New Haven CT, USA.
Pasko RakicDepartment of Neuroscience, Yale University, New Haven CT, USA.
Gabriel SantpereHospital del Mar Research Institute, Parc de Recerca Biomèdica de Barcelona, Catalonia, Spain.
Seth A AmentUniversity of Maryland, Institute for Genome Sciences, Baltimore, MD, USA.
Carlo ColantuoniDepts. of Neurology and Neuroscience Johns Hopkins School of Medicine, Baltimore, MD, USA.ORCID 0000-0001-6818-6380
University of Maryland, Baltimore · USJohns Hopkins University · USYale University · USUniversity of Toronto · CABarcelona Biomedical Research Park · ESNational Institutes of Health · USUniversitat Pompeu Fabra · ES

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
Multi-Omic and Functional Analyses for Hearing Preservation and RestorationZIADC000094 · NIDCD · NATIONAL INSTITUTE ON DEAFNESS AND OTHER COMMUNICATION DISORDERS · PI HERTZANO, RONNA · 2023 to 2025
$10.3M
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

Vast quantities of multi-omic data have been produced to characterize the development and diversity of cell types in the cerebral cortex of humans and other mammals. To more fully harness the collective discovery potential of these data, we have assembled gene-level transcriptomic data from 188 published studies of neocortical development, including the transcriptomes of ~30 million single-cells, extensive spatial transcriptomic experiments and RNA sequencing of sorted cells and bulk tissues: nemoanalytics.org/landing/neocortex. Applying joint matrix decomposition (SJD) to mouse, macaque and human data in this collection, we defined transcriptome dynamics that are conserved across mammalian neurogenesis and which elucidate the evolution of outer, or basal, radial glial cells. Decomposition of adult human neocortical data identified layer-specific signatures in mature neurons and, in combination with transfer learning methods in NeMO Analytics, enabled the charting of their early developmental emergence and protracted maturation across years of postnatal life. Interrogation of data from cerebral organoids demonstrated that while broad molecular elements of

Identifiers

PMID38464021
PMCPMC10925183
OpenAlexW4392344511

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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.