Spatial multi-omic profiling of acute interstitial nephritis: imaging mass cytometry and Xenium spatial transcriptomics datasets

Processed spatial multi-omic data accompanying Baker, Kakade et al., "Spatial analysis reveals the cellular microenvironments and mechanisms of inflammation and kidney injury in acute interstitial nephritis." Manuscript under revision at Nature Communications. This deposit contains five files: 1. xenium_AIN_for_deposit.rds — Seurat v5 object with 321,333 cells from 20 kidney biopsies (8 AIN, 7 ATI, 5 reference) profiled by 10x Genomics Xenium spatial transcriptomics with the Prime 5K Human Pan Tissue & Pathways Panel plus 100 custom kidney genes. Includes Harmony-corrected embeddings, cell-type annotations, T cell and macrophage subtype annotations, and per-cell clinical metadata. 2. imc_yale_discovery_for_deposit.rds — SpatialExperiment object with 1,331,664 cells from the 65-patient discovery cohort (22 AIN, 21 ATI, 22 reference) profiled by imaging mass cytometry with a 31-marker antibody panel. 3. imc_jhu_validation_for_deposit.rds — SpatialExperiment object with 1,216,118 cells from the 41-patient validation cohort (15 AIN, 16 ATI, 10 reference) processed by the same IMC pipeline at Johns Hopkins University. 4. xenium_clinical_metadata_for_deposit.csv — per-patient clinical metadata for the 20 Xenium patients, including baseline / nadir / 6-month eGFR, percent recovery, drug etiology, and demographics. 5. imc_clinical_metadata_for_deposit.csv — per-patient clinical metadata for all 106 IMC patients (combined discovery and validation cohorts). Patient identifiers are de-identified throughout: AIN_##_D / ATI_##_D / REF_##_D for the discovery cohort, AIN_##_V / ATI_##_V / REF_##_V for the validation cohort. The 20 patients shared between Xenium and IMC discovery cohorts use matching IDs across both modalities. Cell-type label columns in the IMC objects include both internal working labels (simplified_annotations, core_annotations) and the published cluster names from Supplementary Table 4 of the manuscript (manuscript_label, manuscript_core_label). Analysis code is available on GitHub at https://github.com/megleila/AIN-spatial-analysis and archived on Zenodo separately. Specimens were obtained under Yale IRB protocol 11110009286 and Johns Hopkins IRB protocols IRB00221958 and IRB00090103.