A Multimodal Single-Cell Epigenomic and 3D Genome Atlas of the Human Basal Ganglia

Program
bican
Collection Type
Dynamic
Keywords
Basal Ganglia DNA methylation Chromatin interaction 3D genome Human Brain snm3C-seq

We profiled 203,036 single nuclei from eight dissected basal ganglia subregions using snm3C-seq to jointly measure DNA methylation and 3D chromatin conformation. We integrated these data with prior snm3C-seq and snmC-seq datasets to assemble a joint epigenomic map comprising 267,662 cells, 1,247 clusters, and 30 cross-modality–defined subclasses from seven donors.

Data citation
No data citation listed
Funding agency
NIMH
Grant numbers
UM1MH130994
Access
open
License
CC BY 4.0

Download URLs

  • Browse HTTP server https://data.nemoarchive.org/bican/grant/BICAN_Mul_PN_Human/salk_ecker/epigenome/nuclei/m3C_seq/human/demultiplexed_fastq/
    Raw HTTP

Anatomical Regions

  • basal ganglia

Taxa

human

Projects this collection belongs to

Assays, Modalities & Techniques

Assays
whole genome spatial transcriptome chromatin methylation
Modalities
genome epigenome
Techniques
m3c-seq whole genome sequencing

Child collections

  • nemo:col-fnhiqmx
    bican__BICAN_Mul_PN_Human__salk_ecker__nuclei__m3C-seq__human__demultiplexed_fastq__open__no_restriction__2026-08-11

Parent collections

Associated publications

  • Chromatin Dynamics and DNA Methylation in Single Cells from Human Basal Ganglia

URL Protocols

No protocol URLs listed for this collection.

Contributors

Show 52 more contributors
  • Cindy Tatiana Báez-Becerra No affiliation listed
  • Jonathan A Rink No affiliation listed
  • Anna Bartlett No affiliation listed
  • Qiurui Zeng Salk Institute for Biological Studies
  • Ruoxuan Wang No affiliation listed
  • Rosa Gomez Castanon No affiliation listed
  • Joseph Nery Salk Institute for Biological Studies 0000-0003-0153-5659
  • Emma Osgood No affiliation listed
  • William Owens No affiliation listed
  • Alaina Petrella No affiliation listed
  • Chumo Chen No affiliation listed
  • Andrea Saldana Acerbo No affiliation listed
  • Ariana S Barcoma No affiliation listed
  • Jiayi Liu No affiliation listed
  • Kaitlyn G Russo No affiliation listed
  • Kyle W Knutson No affiliation listed
  • Carissa K Young No affiliation listed
  • Jackson K Willier No affiliation listed
  • Cesar Barragan No affiliation listed
  • Jessica Arzavala No affiliation listed
  • Silvia Cho No affiliation listed
  • Jordan Altshul No affiliation listed
  • Derek Chan No affiliation listed
  • Eshaan Soma No affiliation listed
  • Jammy Luo No affiliation listed
  • Manya Jain No affiliation listed
  • Sarah Velazquez No affiliation listed
  • Natalie Schenker-Ahmed No affiliation listed
  • Guha V Sundaram No affiliation listed
  • Austin C Manning No affiliation listed
  • Yareli Sanchez No affiliation listed
  • Aleksandra Bikkina No affiliation listed
  • Shuai Fu No affiliation listed
  • Wei Tian Salk Institute for Biological Studies
  • Huaming Chen Salk Institute for Biological Studies
  • Yueyue Wu No affiliation listed
  • Manoj Hariharan No affiliation listed
  • Carolyn O’Connor No affiliation listed
  • Michelle Liem No affiliation listed
  • Mikayla V Marrin No affiliation listed
  • Cynthia Rose No affiliation listed
  • Shane N Alt No affiliation listed
  • Jillian Berry No affiliation listed
  • Wenjin Zhang No affiliation listed
  • Quan Zhu No affiliation listed
  • Rebecca D Hodge No affiliation listed
  • Trygve Bakken Allen Institute 0000-0003-3373-7386
  • Ed S Lein Allen Institute 0000-0001-9012-6552
  • Daofeng Li No affiliation listed
  • Ting Wang Washington University School of Medicine 0000-0002-6800-242X
  • Xiangmin Xu University of California, Irvine 0000-0002-5828-1533
  • Bing Ren University of California, San Diego 0000-0002-5435-1127

Cross-archive links

No cross-archive links listed for this collection.

Documentation & resources