Processed single nucleus data of Arabidopsis thaliana leaves infected by Sclerotinia sclerotiorum

Processed single nucleus data of Arabidopsis thaliana leaves infected by Sclerotinia sclerotiorum (24hpi). sc_jones2025.Rds and sc_jones2025.RData are identical R objects that can be loaded using either readRDS or load (as preferred). The data is stored as a SingleCellExperiment object which can easily be converted to other common formats (e.g. Seurat). Minimal steps to load the dataset in R are: if (!require("BiocManager", quietly = TRUE)) { install.packages("BiocManager") } BiocManager::install("SingleCellExperiment") load("sc_jones2025.RData") # creates object sc_jones2025 # or sc_jones2025 <- readRDS("sc_jones2025.Rds") library(SingleCellExperiment) colData(sc_jones2025) rowData(sc_jones2025) reducedDimNames(sc_jones2025) colData contains cluster and celltype assignments for each nucleus under e.g. cluster_l1 and cluster_l1_celltypes, for the level 1 clusters. The main datasets used in the manuscript are accessible by: reducedDim(sc_jones2025, "HARMONY") reducedDim(sc_jones2025, "HARMONY.TSNE")reducedDim(sc_jones2025, "CNMF") assay(sc_jones2025, "counts") assay(sc_jones2025, "logcounts") assay(sc_jones2025, "normcounts") For those not using R or if compatibility issues arise, these main datasets and associated column and row data are also included as tsv files in sc_jones2025_tsvs.zip. Tables can be joined by either the "gene" or "cell" columns.