Title : Uncovering the Molecular Logic of Cortical Wiring between Neuronal subtypes Across Development Through Ligand–Receptor Inference

Title : Uncovering the Molecular Logic of Cortical Wiring between Neuronal subtypes Across Development Through Ligand–Receptor Inference

Authors: Rémi Mathieu¹, Tangra Draia-Nicolau¹, Léa Corbières¹, Annousha Govindan¹, Vianney Bensa¹, Emilie Pallesi-Pocachard¹, Lucas Silvagnoli¹, Alfonso Represa¹, Carlos Cardoso¹, Ludovic Telley^{2 3}*& Antoine de Chevigny¹*

This repository contains all materials used to generate the figures and data products presented in our study, as well as the source objects displayed in the associated Shiny dashboard.

Contents

• Script.zip
  Contains the full workflow script used to process the data and generate all figures included in the manuscript. This file provides the complete code pipeline for reproducibility.

• Data.zip
  Includes the processed data objects that are visualized in the Shiny dashboard. These objects represent the final curated datasets used for analysis and interactive exploration.

• intermediate_plot_Assignid_used_in_paper.zip
  Contains intermediate QC (quality-control) PDF files generated during the data processing steps. These plots document key checks performed throughout the workflow to ensure data quality and transparency.

Raw Data Availability

Raw single-cell RNA-seq data are publicly available in ArrayExpress under accession E-MTAB-16260 (single-cell) and E-MTAB-16355 (single-nucleus), accessible via the BioStudies portal: https://www.ebi.ac.uk/biostudies/arrayexpress/studies