A Multiomic (RNA + ATAC) Atlas of Human Basal Ganglia and Cortical Development from Mid-Gestation Through Early Infancy

Program
bican
Collection Type
Dynamic
Keywords
Basal Ganglia human development neural progenitors single-cell multiome

10x Genomics single-cell multiome (RNA + ATAC) dataset (> 400k nuclei) generated from human basal ganglia and cortical tissue spanning key developmental windows, including mid-gestation, prematurely delivered third-trimester infants, and postnatal ages (1 month and 7 months). Tissue samples were obtained from the caudate nucleus, putamen, and globus pallidus, as well as frontal, parietal, and temporal cortical regions. Paired gene expression and chromatin accessibility profiles were derived from each nucleus, with donors contributing one or multiple regions depending on case. For each library preparation, nuclei from two donor samples were pooled and processed together to increase capture efficiency. Following sequencing, sample identities were resolved through computational demultiplexing using genotype-based assignment. Comprehensive metadata accompany the dataset, including donor characteristics, regional identity, sequencing batch and cell type annotations.

Data citation
No data citation listed
Funding agency
NIMH
Grant numbers
U01MH130995
Access
open
License
No license listed

Download URLs

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Anatomical Regions

  • basal nuclei (basal ganglia)
  • cerebral cortex

Taxa

human

Projects this collection belongs to

  • nemo:prj-vwtwc3r
    Spatiotemporal epigenomic and chromosomal architectural cell atlas of developing human brains

Assays, Modalities & Techniques

Assays
multiome; chromatin multiome; transcriptome
Modalities
multimodal
Techniques
10X genomics multiome;atac-seq 10X genomics multiome;rnaseq

Child collections

No child collections listed for A Multiomic (RNA + ATAC) Atlas of Human Basal Ganglia and Cortical Development from Mid-Gestation Through Early Infancy collection.

Parent collections

Associated publications

No publications linked yet.

URL Protocols

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Contributors

  • Gaurav Singh Rathore No affiliation listed
  • Oier Pastor-Alonso No affiliation listed 0000-0001-8075-1768
  • Abbey Green No affiliation listed
  • Mohammad Baig No affiliation listed
Show 8 more contributors
  • Rayyan G Irfan No affiliation listed
  • Selina Li No affiliation listed
  • I-ling Lu No affiliation listed
  • Jaeyeon Kim No affiliation listed
  • Jason Ernst No affiliation listed
  • Eran A Mukamel University of California, San Diego 0000-0003-3203-9535
  • Chongyuan Luo University of California, Los Angeles 0000-0002-8541-0695
  • Mercedes F Paredes No affiliation listed

Cross-archive links

No cross-archive links listed for this collection.

Documentation & resources