AllenInstitute/DNA-sequence-model

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} }