This repository contains the code used for the processing and analysis of the single-cell RNA-sequencing datasets presented in our study investigating an environmentally regulated cell state (ERS) across Arabidopsis thaliana root cell lineages.
Oliva M. et al. (2026). An environmentally regulated dichotomy in cell lineages of the root.
[Link to publication]
Scripts used for processing sequencing datasets and generating the objects used for downstream analyses.
pre-processing_per_library/– pre-processing and quality control of individual scRNA-seq libraries.integration/– integration of libraries for the different datasets and experimental comparisons used in the study.
Further information is provided in data/README.md.
Scripts used for downstream analyses presented in the manuscript.
A correspondence between analysis scripts and manuscript figures is provided in analyses/README.md.
Raw FASTQ files generated in this study have been deposited in the European Nucleotide Archive (ENA) under Project accession PRJEB100815.
Processed Seurat objects used for downstream analyses have been deposited on Zenodo under the following DOIs:
Previously published datasets reanalysed in this study are available from their original repositories. Details and accession information are provided in the Methods of the associated manuscript.
Software and package versions used for data processing and analysis are described in the Methods of the associated manuscript.
For questions regarding the code or analyses, please contact:
Marina Oliva
marina.oliva@uwa.edu.au