Data for: Tissue-adapted NK cells shape pathogenic cDC1 niches in early arthritis

Dataset reference

This repository contains the patient-pseudonymised CITE-seq data required to reproduce the findings of our study on the early innate immune landscape of treatment-naïve juvenile idiopathic arthritis (JIA).

Count matrices

These archives contain the 10x Cell Ranger multi output and CellBender-corrected count matrices.

output_Knight_2026.tar.gz

output_Bolton_2025.tar.gz

Gene expression reads were mapped to an optimised reference transcriptome using the OSCAR pipeline, and ADT reference files can be found within each library's output.

Seurat objects

Processed, integrated, and annotated objects. The Seurat (v5) objects have been serialised using the qs2 format for speed and interoperability, rather than .rds.

seurat_JIA_global_cells.qs2

seurat_JIA_innate_lymphocytes.qs2

seurat_JIA_dendritic_cells.qs2

Reading .qs2 files in R: To read these files into R, you need to use the qs2 package (https://github.com/qsbase/qs2).

library(qs2)
seurat_object <- qs_read("filename.qs2")

AnnData objects

Python-native objects. For browser-based interactive exploration of these datasets without downloading local files, you can visit our integrated collection on CELLxGENE.

anndata_JIA_global_cells.h5ad

anndata_JIA_innate_lymphocytes.h5ad

anndata_JIA_dendritic_cells.h5ad

Citation guidelines: 

Please cite the appropriate manuscripts based on the specific datasets analysed:

For the innate lymphocyte or dendritic cell datasets: Please cite our primary manuscript: https://www.biorxiv.org/content/10.64898/2026.05.01.716870v1.

For the mononuclear cell data from blood and synovial fluid: Please cite both our manuscript and Bolton, Mahony et al., 2025 (Sci Transl Med; DOI: 10.1126/scitranslmed.adt6050).

For analyses specifically isolating or utilising the synovial tissue data: Please cite Bolton, Mahony et al., 2025 (Sci Transl Med; DOI: 10.1126/scitranslmed.adt6050).