PD-L1-linked spatial architecture of immune evasion in EBV-positive diffuse large B-cell lymphoma

This dataset contains processed single-cell and spatial profiling data from EBV-positive diffuse large B-cell lymphoma (EBV+ DLBCL) tumor tissue, generated at the University of Lübeck, Germany, in support of the study "PD-L1-linked spatial architecture of immune evasion in EBV-positive diffuse large B-cell lymphoma." Raw sequencing data (scRNA-seq and Visium FASTQs) are available under controlled access at the European Genome-phenome Archive (EGA): EGAD50000002792 and EGAD50000002791. ## Files **EBV_DLBCL_scRNA_Seurat.rds**Seurat v5 object for single-cell RNA sequencing data from 10 EBV+ DLBCL cases (112,834 cells after QC filtering and doublet removal). Samples were profiled using the 10x Genomics Chromium platform on FFPE tumor tissue. Cells were multiplexed into three pools and sequenced on an Illumina NovaSeq 6000. Per-sample demultiplexing was performed using Cell Ranger multi (v7.2.0). Downstream analysis was performed in Seurat v5 with Harmony batch correction and ProjecTILs cell type annotation. Key metadata columns: public_sample_id, Pool, PDL1_CD274, Condition, Annotation_V4, percent.mt, diagnosis, tissue, platform. Dimensionality reductions included: PCA, UMAP (Harmony-integrated). --- **Visium_data.zip**Space Ranger v3.1.0 output and per-sample Seurat objects for 18 EBV+ DLBCL cases profiled using the 10x Genomics Visium for FFPE Gene Expression platform on an Illumina NovaSeq 6000. Raw reads were processed with Space Ranger v3.1.0 (GRCh38). Downstream analysis was performed in Seurat v5 with SpotClean preprocessing. Structure per sample: SpaceRanger/{SAMPLE_ID}/ filtered_feature_bc_matrix.h5 raw_feature_bc_matrix.h5 molecule_info.h5 metrics_summary.csv web_summary.html spatial/ tissue_lowres_image.png scalefactors_json.json tissue_positions.csv Seurat/ visium_seurat_{SAMPLE_ID}.rds --- **CosMx_data.zip**Raw AtoMx export files and annotated Seurat object for 10 EBV+ DLBCL cases profiled using the NanoString CosMx Spatial Molecular Imager with the Human Protein Immuno-Oncology Panel v1.2 (62 proteins). Data were processed using AtoMx and analyzed in Seurat v5 with Harmony batch correction (CLR normalization, 57 biological proteins). Structure: CosMx_Protein_OT1/ CosMx_OT1_exprMat_file.csv.gz Protein expression matrix CosMx_OT1_metadata_file.csv.gz Per-cell metadata and QC metrics CosMx_OT1_fov_positions_file.csv.gz Field-of-view spatial positions CosMx_OT1-polygons.csv.gz Cell segmentation polygons CosMx_Protein_OT2/ (same structure as OT1) cosmx_seurat_annotated.rds Merged, batch-corrected, annotated Seurat object ## Sample information ### scRNA-seq (10 samples, 3 pools) | Sample ID | Pool | PDL1 CNA | Morphology ||------------|------|----------|-------------|| DLBCL_01_1 | P2 | wt | monomorphic || DLBCL_04_1 | P2 | wt | polymorphic || DLBCL_06_1 | P2 | wt | monomorphic || DLBCL_09_1 | P1 | Del | polymorphic || DLBCL_10_1 | P1 | Del | polymorphic || DLBCL_16_2 | P3 | Amp | monomorphic || DLBCL_17_1 | P1 | wt | monomorphic || DLBCL_22_1 | P3 | Amp | polymorphic || DLBCL_25_1 | P1 | wt | polymorphic || DLBCL_27_1 | P2 | Amp | monomorphic | Pool composition:- Pool 1 (EBVDLBCL_P1): DLBCL_17_1, DLBCL_09_1, DLBCL_10_1, DLBCL_25_1- Pool 2 (EBVDLBCL_P2): DLBCL_01_1, DLBCL_04_1, DLBCL_06_1, DLBCL_27_1- Pool 3 (EBVDLBCL_P3): DLBCL_22_1, DLBCL_16_2 --- ### Visium spatial transcriptomics (18 QC-passing samples) DLBCL_04_1, DLBCL_05_1, DLBCL_06_1, DLBCL_08_1, DLBCL_09_1, DLBCL_10_1,DLBCL_16_1, DLBCL_17_1, DLBCL_18_1, DLBCL_19_1, DLBCL_20_1, DLBCL_23_1,DLBCL_24_2, DLBCL_25_1, DLBCL_26_1, DLBCL_28_1, DLBCL_29_1, DLBCL_30_2 --- ### CosMx single-cell spatial proteomics (10 samples, 2 slides) Panel: NanoString Human Protein Immuno-Oncology Panel v1.2 (62 proteins) Slide OT1:| FOV range | Sample ID ||-----------|------------|| 001–090 | DLBCL_25_1 || 091–154 | DLBCL_06_1 || 155–224 | DLBCL_10_1 || 225–283 | DLBCL_01_1 || 284–391 | DLBCL_18_1 || 392–461 | DLBCL_27_1 | Slide OT2:| FOV range | Sample ID ||-----------|------------|| 001–102 | DLBCL_13_1 || 103–136 | DLBCL_17_1 || 137–174 | DLBCL_09_1 || 175–305 | DLBCL_16_1 || 306–390 | DLBCL_22_1 | ## Citation Please cite the associated manuscript when using these data:Künstner A et al. "PD-L1-linked spatial architecture of immune evasion in EBV-positive diffuse large B-cell lymphoma."