Preprocessed single-cell RNA-seq and CITE-seq count data from: Single-cell profiling of BAL in preschool cystic fibrosis reveals macrophage dysregulation and ivacaftor-modified inflammatory programs in the early life lung

Preprocessed single-cell RNA-seq and CITE-seq count data from bronchoalveolar lavage (BAL) samples collected from paediatric cystic fibrosis (CF) and non-CF control subjects, generated for the study: "Single-cell profiling of BAL in preschool cystic fibrosis reveals macrophage dysregulation and ivacaftor-modified inflammatory programs in the early life lung" (Maksimovic et al., Mucosal Immunology, 2026; https://doi.org/10.1016/j.mucimm.2026.03.012). The archive contains preprocessed SingleCellExperiment (SCE) objects in RDS format for each of 7 sequencing batches (batch 0–6), produced using the 10x Chromium platform and processed with the CellRanger pipeline. These objects represent the earliest stage of processing that can be shared openly: empty droplets have been called and samples demultiplexed, but upstream steps requiring participant genetic information for demultiplexing are not included. Processed and annotated single-cell data are available for exploration on CELLxGENE at https://cellxgene.cziscience.com/collections/30704a65-1b50-409b-9cf6-1f26bf644c99. All analysis code is available at https://github.com/Oshlack/paediatric-cf-inflammation-citeseq and archived on Zenodo at https://doi.org/10.5281/zenodo.19381224.