scRNA-seq Analysis Pipeline for Dictyostelium Developmental Synchronicity
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2026
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| _version_ | 1866902322236358656 |
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| author | Lena Trnovec |
| author_facet | Lena Trnovec |
| contents | <h1>Release v1.0.0</h1> <p>This release accompanies the manuscript <strong>"Early cAMP signaling orchestrates single-cell synchronicity throughout Dictyostelium development"</strong> by Katoh-Kurasawa, Trnovec et al.</p> <h2>Overview</h2> <p>This repository provides a comprehensive analysis pipeline for single-cell RNA sequencing (scRNA-seq) data from <em>Dictyostelium discoideum</em>, focusing on quantifying developmental synchronicity at single-cell resolution.</p> <h2>Key Features</h2> <h3>Analysis Pipeline</h3> <ul> <li><strong>Quality Control</strong> (<code>01_quality_control.ipynb</code>): Import raw 10x Genomics counts, perform QC, and filter low-quality cells</li> <li><strong>Comprehensive Analysis</strong> (<code>02_analysis.ipynb</code>): Complete pipeline including dimensionality reduction, clustering, cell-type annotation, and visualization</li> <li><strong>Synchronicity Analysis</strong> (<code>03_synchronicity.ipynb</code>): Quantitative analysis of cell population synchronicity</li> <li><strong>PCA Comparison</strong> (<code>05_pca_comparison.ipynb</code>): Comparative analysis across conditions</li> </ul> <h3>Scientific Contributions</h3> <ul> <li>Quantifies synchronicity at single-cell resolution using scRNA-seq</li> <li>Uses Universal Cell Embedding (UCE) model for unified transcriptome mapping</li> <li>Analyzes wild-type (AX4) and mutant strains (acaA⁻, acaA⁻pkaC⁻)</li> <li>Demonstrates that early cAMP-pulse signaling acts as a metronome for developmental synchronicity</li> <li>Reveals differential synchronicity between prespore and prestalk cells</li> </ul> <h3>Technical Implementation</h3> <ul> <li>Modular and reproducible Python codebase</li> <li>Custom utility functions in <code>src/</code> module</li> <li>UCE-based dimensionality reduction</li> <li>UMAP visualization</li> <li>Cell-type annotation and clustering</li> </ul> <h2>Data Availability</h2> <p>All data is publicly available in the <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE305468">GEO repository</a> with GEO accession number GSE305468.</p> <h2>Installation</h2> <pre><code>git clone https://github.com/lenatr99/scRNA_dicty.git cd scRNA_dicty conda env create -f environment.yml conda activate scRNA_env </code></pre> <h2>Citation</h2> <p>If you use this pipeline or data, please cite:</p> <p>Katoh-Kurasawa, M., Trnovec, L., et al. "Early cAMP signaling orchestrates single-cell synchronicity throughout Dictyostelium development." (2026)</p> <h2>Contributors</h2> <ul> <li>Mariko Katoh-Kurasawa (Baylor College of Medicine)</li> <li>Lena Trnovec (University of Ljubljana)</li> <li>Peter Lehmann (Baylor College of Medicine)</li> <li>Rui Chen (Baylor College of Medicine)</li> <li>Yumei Li (Baylor College of Medicine)</li> <li>Blaz Zupan (University of Ljubljana & Baylor College of Medicine)</li> <li>Gad Shaulsky (Baylor College of Medicine)</li> </ul> <p><strong>Last updated:</strong> February 4, 2026</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_18481808 |
| institution | Zenodo |
| language | |
| publishDate | 2026 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | scRNA-seq Analysis Pipeline for Dictyostelium Developmental Synchronicity Lena Trnovec <h1>Release v1.0.0</h1> <p>This release accompanies the manuscript <strong>"Early cAMP signaling orchestrates single-cell synchronicity throughout Dictyostelium development"</strong> by Katoh-Kurasawa, Trnovec et al.</p> <h2>Overview</h2> <p>This repository provides a comprehensive analysis pipeline for single-cell RNA sequencing (scRNA-seq) data from <em>Dictyostelium discoideum</em>, focusing on quantifying developmental synchronicity at single-cell resolution.</p> <h2>Key Features</h2> <h3>Analysis Pipeline</h3> <ul> <li><strong>Quality Control</strong> (<code>01_quality_control.ipynb</code>): Import raw 10x Genomics counts, perform QC, and filter low-quality cells</li> <li><strong>Comprehensive Analysis</strong> (<code>02_analysis.ipynb</code>): Complete pipeline including dimensionality reduction, clustering, cell-type annotation, and visualization</li> <li><strong>Synchronicity Analysis</strong> (<code>03_synchronicity.ipynb</code>): Quantitative analysis of cell population synchronicity</li> <li><strong>PCA Comparison</strong> (<code>05_pca_comparison.ipynb</code>): Comparative analysis across conditions</li> </ul> <h3>Scientific Contributions</h3> <ul> <li>Quantifies synchronicity at single-cell resolution using scRNA-seq</li> <li>Uses Universal Cell Embedding (UCE) model for unified transcriptome mapping</li> <li>Analyzes wild-type (AX4) and mutant strains (acaA⁻, acaA⁻pkaC⁻)</li> <li>Demonstrates that early cAMP-pulse signaling acts as a metronome for developmental synchronicity</li> <li>Reveals differential synchronicity between prespore and prestalk cells</li> </ul> <h3>Technical Implementation</h3> <ul> <li>Modular and reproducible Python codebase</li> <li>Custom utility functions in <code>src/</code> module</li> <li>UCE-based dimensionality reduction</li> <li>UMAP visualization</li> <li>Cell-type annotation and clustering</li> </ul> <h2>Data Availability</h2> <p>All data is publicly available in the <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE305468">GEO repository</a> with GEO accession number GSE305468.</p> <h2>Installation</h2> <pre><code>git clone https://github.com/lenatr99/scRNA_dicty.git cd scRNA_dicty conda env create -f environment.yml conda activate scRNA_env </code></pre> <h2>Citation</h2> <p>If you use this pipeline or data, please cite:</p> <p>Katoh-Kurasawa, M., Trnovec, L., et al. "Early cAMP signaling orchestrates single-cell synchronicity throughout Dictyostelium development." (2026)</p> <h2>Contributors</h2> <ul> <li>Mariko Katoh-Kurasawa (Baylor College of Medicine)</li> <li>Lena Trnovec (University of Ljubljana)</li> <li>Peter Lehmann (Baylor College of Medicine)</li> <li>Rui Chen (Baylor College of Medicine)</li> <li>Yumei Li (Baylor College of Medicine)</li> <li>Blaz Zupan (University of Ljubljana & Baylor College of Medicine)</li> <li>Gad Shaulsky (Baylor College of Medicine)</li> </ul> <p><strong>Last updated:</strong> February 4, 2026</p> |
| title | scRNA-seq Analysis Pipeline for Dictyostelium Developmental Synchronicity |
| url | https://doi.org/10.5281/zenodo.18481808 |