Evidence map›Paper›PMID 41684930›Full record

ArticlebioRxiv : the preprint server for biology2026

Single-cell Multiome Analysis of Chromatin State and Transcriptome in the Human Basal Ganglia.

Lei Chang, Kai Li, Yang Xie, Guojie Zhong, Jonathan A Rink, Cindy Tatiana Báez-Becerra, Audrey Lie, Hannah S Indralingam, Keyi Dong, Timothy Loe and 50 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2026. 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.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

60 authors.

Lei ChangDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
Kai LiDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
Yang XieDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
Guojie ZhongNew York Genome Center, New York, NY, USA.
Jonathan A RinkComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Cindy Tatiana Báez-BecerraComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Audrey LieDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
Hannah S IndralingamDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
Keyi DongDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
Timothy LoeDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
Zhaoning WangDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
Songpeng ZuDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
Joseph Colin KernCenter for Epigenomics, University of California, San Diego, La Jolla, CA, USA.
Zoey ZhaoCenter for Epigenomics, University of California, San Diego, La Jolla, CA, USA.
Eric BooneCenter for Epigenomics, University of California, San Diego, La Jolla, CA, USA.
Jesus FloresCenter for Epigenomics, University of California, San Diego, La Jolla, CA, USA.
Alexander MonellCenter for Epigenomics, University of California, San Diego, La Jolla, CA, USA.
Jacqueline OlnessCenter for Epigenomics, University of California, San Diego, La Jolla, CA, USA.
Cesar BarraganGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Emma OsgoodGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
William OwensGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Natalie Schenker-AhmedGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Wenjin ZhangDepartment of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
Di LiuDepartment of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA.
Ariana S BarcomaComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Jackson K WillierComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Kyle W KnutsonComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Kaitlyn G RussoComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Jiayi LiuComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Silvia ChoComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Jessica ArzavalaComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Carissa K YoungComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Guha V SundaramComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Austin C ManningComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Yareli SanchezComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Aleksandra BikkinaComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Jillian BerryDepartment of Pathology and Laboratory Medicine, University of California, Irvine, CA, USA.
Xiaomeng GaoDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
Carolyn O'ConnorFlow Cytometry Core Facility, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Michelle LiemFlow Cytometry Core Facility, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Mikayla V MarrinFlow Cytometry Core Facility, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Cynthia RoseFlow Cytometry Core Facility, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Shane N AltFlow Cytometry Core Facility, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Chenxu ZhuNew York Genome Center, New York, NY, USA.
Nathan R ZemkeCenter for Epigenomics, University of California, San Diego, La Jolla, CA, USA.
Wubin DingGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Amit KleinGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Yuanyuan FuAllen Institute for Brain Science, Seattle, WA, USA.
Nelson JohansenAllen Institute for Brain Science, Seattle, WA, USA.
Trygve E BakkenAllen Institute for Brain Science, Seattle, WA, USA.
Rebecca D HodgeAllen Institute for Brain Science, Seattle, WA, USA.
C Dirk KeeneUniversity of Washington, Seattle, WA, USA.
Ed S LeinAllen Institute for Brain Science, Seattle, WA, USA.
Daofeng LiDepartment of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
Quan ZhuCenter for Epigenomics, University of California, San Diego, La Jolla, CA, USA.
Ting WangDepartment of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
Xiangmin XuDepartment of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA.
Joseph R EckerGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
M Margarita BehrensComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Bing RenDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.

Funding

Center for Multiomic Human Brain Cell AtlasUM1MH130994 · NIMH · SALK INSTITUTE FOR BIOLOGICAL STUDIES · PI MARIA MARGARITA BEHRENS, Joseph R Ecker · 2022 to 2026
$92.4M
University of Washington Alzheimer's Disease Research CenterP30AG066509 · NIA · UNIVERSITY OF WASHINGTON · PI SUMAN JAYADEV · 2020 to 2026
$29.0M
Spectral Configured Bigfoot Sorter for Salk Institute Flow Cytometry CoreS10OD034268 · OD · SALK INSTITUTE FOR BIOLOGICAL STUDIES · PI O'CONNOR, CAROLYN PEY-MIN · 2023 to 2023
$724k
BD FACSAria Fusion for Flow Cytometry Core FacilityS10OD023689 · OD · SALK INSTITUTE FOR BIOLOGICAL STUDIES · PI ZHENG, YE · 2018 to 2018
$530k
NIA NIH HHS P30 AG066509NIH HHS S10 OD023689NIH HHS S10 OD034268NIMH NIH HHS UM1 MH130994
6 · The paper itself

Abstract

The basal ganglia play essential roles in motor control, emotion, learning and reward processing. Their dysfunction contributes to many neurological and psychiatric disorders. However, the gene regulatory programs defining basal ganglia cell-type identity and function remain poorly understood, limiting interpretation of disease-associated non-coding variants. Here, we present the first single-cell multiome atlas of histone modifications and transcriptomes across eight basal ganglia regions from neurotypical adult human donors. Joint profiling reveals cell-type-specific deployment of active and repressive

Indexed as

chromatin conformationdeep learning modelepigenomeH3K27acH3K27me3H3K9me3neurological disordersPaired-Tagpsychiatric diseasesSingle-cell histone modifications

Identifiers

PMID41684930
PMCPMC12893060

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

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.