| --- |
| 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} |
| } |
| |
