README.md

---
license: mit
tags:
- neuroscience
- genomics
- dna
- sequence-modeling
- basal-ganglia
- spinal-cord
- astrocyte
- regulatory-genomics
pretty_name: DNA Sequence Modeling for BG Cell Atlas Package
---

# DNA Sequence Modeling for the Basal Ganglia Cell Atlas Package

This repository contains DNA-sequence modeling resources associated with the basal ganglia (BG) cell atlas package. It serves as a centralized entry point for sequence-based regulatory analyses across multiple companion studies.

## What this repository is

This repository is a landing page and resource hub for DNA-sequence modeling analyses associated with the basal ganglia cell atlas package.

## What this repository is not

This repository is not intended to duplicate the full analysis pipelines of the companion studies. Instead, it provides a centralized entry point for sequence-modeling-related resources, outputs, and links.

## Overview

Across these studies, sequence-based modeling is used to investigate cis-regulatory logic underlying cell type specialization. These analyses complement multiomic profiling (snRNA-seq, snATAC-seq, spatial transcriptomics, methylation, and chromatin conformation) by providing a sequence-level perspective on candidate enhancers and regulatory programs.

## Associated studies

### 1. Basal ganglia consensus taxonomy  
**Johansen, Fu et al., 2025**

This study establishes a consensus basal ganglia taxonomy by integrating HMBA single-nucleus RNA-seq data from human, macaque, marmoset, and previously published mouse datasets. The resulting framework provides a standardized naming system for basal ganglia cell types, enabling cross-species comparison, community-wide adoption, and downstream tool development.

### 2. Cross-species spinal cord atlas  
**Schmitz, Johansen et al., 2026**

This study presents a unified cross-species atlas integrating single-nucleus multiomic profiling and spatial transcriptomics across human, macaque, and mouse. In addition to defining a conserved cell type hierarchy, it links molecular identities to anatomical organization and cis-regulatory programs, including sequence-based modeling of enhancer logic.

### 3. Human BG astrocyte subgroup study  
**Fu et al., 2026**

This study identifies three major astrocyte subgroups in the human basal ganglia and characterizes their spatial, molecular, and regulatory specialization. Sequence-based modeling is used to evaluate subgroup-associated regulatory elements and candidate enhancer programs.

## Repository contents

Depending on the final organization, this repository include:
- model configuration files  
- input sequence sets (candidate regulatory regions)  
- cell type-enriched regions  
- model predictions and scoring outputs  
- motif and enhancer-level summaries  
- example loci used in the manuscript  

## Conceptual workflow

1. Define candidate regulatory regions from multiomic data  
2. Extract DNA sequences for modeling  
3. Train or apply sequence-based models  
4. Score sequences for regulatory activity  
5. Interpret subgroup- or cell type-specific regulatory patterns  

## Links

- Basal ganglia consensus taxonomy paper: [add link]  
- Spinal cord consensus atlas paper: [add link]  
- Basal ganglia astrocyte study: [add link]  
- Multiomic track viewer (SCMDAP): [add link]  
- Project GitHub repository: [add link]  

## Citation

Please cite the relevant companion manuscripts when using these resources.

@article{BG_PACKAGE,
  title   = {Cross-species consensus atlas of the primate basal ganglia},
  author  = {Johansen, Nelson and Fu, Yuanyuan and others},
  journal = {bioRxiv},
  year    = {2025}
}

@article{BG_PACKAGE,
  title   = {A consensus spinal cord cell type atlas across mouse, macaque, and human},
  author  = {Schmitz, Matthew and Johansen, Nelson and others},
  journal = {bioRxiv},
  year    = {2026}
}

@article{BG_PACKAGE,
  title   = {Circuit-dependent specialization of human basal ganglia astrocytes},
  author  = {Fu, Yuanyuan and others},
  journal = {bioRxiv},
  year    = {2025}
}