Evidence map›Paper›PMID 41659532›Full record

ArticlebioRxiv : the preprint server for biology2026

An Integrated Single-Cell and Epigenomic Resource for Comparative Analysis of the Basal Ganglia.

Wenjin Zhang, Wubin Ding, Kai Li, Lei Chang, Amit Klein, Cindy Tatiana Báez-Becerra, Jonathan A Rink, Anna Bartlett, Huaming Chen, Natalie Schenker and 19 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

29 authors.

Wenjin ZhangDepartment of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.
Wubin DingGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Kai LiDepartment of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA.
Lei ChangDepartment of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA.
Amit KleinGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Cindy Tatiana Báez-BecerraComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Jonathan A RinkComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Anna BartlettGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Huaming ChenGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Natalie SchenkerGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Nelson JohansenAllen Institute for Brain Science, Seattle, WA, 98109, USA.
Tyler MollenkopfAllen Institute for Brain Science, Seattle, WA, 98109, USA.ORCID 0000-0002-2899-2879
Yuanyuan FuAllen Institute for Brain Science, Seattle, WA, 98109, USA.
Xie YangDepartment of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA.
Shane LiuDepartment of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.
Chanrung SengDepartment of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.
Benpeng MiaoDepartment of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.
Tianjie LiuDepartment of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.
Quan ZhuCenter for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego; La Jolla, CA, USA.
Rebecca D HodgeAllen Institute for Brain Science, Seattle, WA, 98109, USA.ORCID 0000-0002-5784-9668
Trygve E BakkenAllen Institute for Brain Science, Seattle, WA, 98109, USA.ORCID 0000-0003-3373-7386
Ed S LeinAllen Institute for Brain Science, Seattle, WA, 98109, USA.
Michael HawrylyczAllen Institute for Brain Science, Seattle, WA, 98109, USA.
Xiangmin XuDepartment of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA.
M Margarita BehrensComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Bing RenDepartment of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA.
Joseph R EckerGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Ting WangDepartment of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.
Daofeng LiDepartment of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.ORCID 0000-0001-7492-3703

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
NIMH NIH HHS UM1 MH130994
6 · The paper itself

Abstract

The basal ganglia regulate motor, cognitive, and affective behaviors, and their dysfunction underlies diverse neurological and psychiatric disorders. Comprehensive, accessible multi-omics resources are needed to understand the regulatory mechanisms governing basal ganglia cell types. Here we present an open, interactive web-based platform for exploring single-cell multi-omics datasets from basal ganglia, generated using 10X Multiome, snm3C-seq, and Paired-Tag technologies from the BICAN (NIH BRAIN Initiative Cell Atlas Network) consortium. The platform is available at https://basalganglia.epigenomes.net/ and enables integrated visualization of gene expression, chromatin accessibility, DNA methylation, histone modifications, and chromatin conformation across cell types and human, macaque, marmoset, and mouse species, with direct genome browser support and comparative epigenomic functionality. Representative analyses demonstrate cell-type-specific regulatory landscapes, conserved and species-specific regulatory elements, and links between epigenomic regulation and transcription. This resource provides a scalable, community-oriented foundation for advancing basal ganglia biology and interpreting regulatory mechanisms relevant to brain function and disease.

Indexed as

Basal gangliaComparative epigenomicsData visualizationSingle cell epigenomics

Identifiers

PMID41659532
PMCPMC12873978

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.