scRNA-seq Analysis Pipeline for Dictyostelium Developmental Synchronicity

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