A.K. Basak

Follicular Lymphoma Transformation is Characterized by Cytokine-associated Remodeling of Stromal and Macrophage Compartments

Nicholas J. Haradhvala, Stephanie Pei Tung Yiu, Laura Beckmann, Sam Sadigh et autres

Across cancer, one of the most frequent examples of histologic transformation is the evolution of follicular lymphoma (FL) to an aggressive large cell lymphoma. Despite recent progress, understanding of the molecular and cellular underpinnings of transformation remains incomplete. Here, we dissect the …

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Supp Table 9 from Same-Slide Spatial Multiomics Integration with IN-DEPTH Reveals Tumor Virus–Linked Spatial Reorganization of the Tumor Microenvironment

Stephanie Pei Tung Yiu, Yuzhou Chang, Yao Yu Yeo, Huaying Qiu et autres

Enrichment pathways in LMP1-positive and LMP1-negative tumors and their neighboring macrophages.

Supp Table 10 from Same-Slide Spatial Multiomics Integration with IN-DEPTH Reveals Tumor Virus–Linked Spatial Reorganization of the Tumor Microenvironment

Stephanie Pei Tung Yiu, Yuzhou Chang, Yao Yu Yeo, Huaying Qiu et autres

Mean expression, statistical metrics, and Log2fold change of ligand-receptor interactions.

Supp Table 11 from Same-Slide Spatial Multiomics Integration with IN-DEPTH Reveals Tumor Virus–Linked Spatial Reorganization of the Tumor Microenvironment

Stephanie Pei Tung Yiu, Yuzhou Chang, Yao Yu Yeo, Huaying Qiu et autres

Patient metadata for the DLBCL cohorts included in this study.

Supp Table 1 from Same-Slide Spatial Multiomics Integration with IN-DEPTH Reveals Tumor Virus–Linked Spatial Reorganization of the Tumor Microenvironment

Stephanie Pei Tung Yiu, Yuzhou Chang, Yao Yu Yeo, Huaying Qiu et autres

Details of the antibody panel used in all IN-DEPTH experiments throughout the study including antibody clones, vendors, working concentrations, imaging channel, imaging cycle and exposure time.

Data from Same-Slide Spatial Multiomics Integration with IN-DEPTH Reveals Tumor Virus–Linked Spatial Reorganization of the Tumor Microenvironment

Stephanie Pei Tung Yiu, Yuzhou Chang, Yao Yu Yeo, Huaying Qiu et autres

Abstract Spatial transcriptomics and proteomics have enabled profound insights into tissue organization, yet these technologies remain largely disparate, and emerging same-slide multiomics approaches are limited in plex, spatial resolution, signal retention, and integrative analytics. We introduce IN-situ DEtailed Phenotyping To High-resolution transcriptomics …

Supp Table 5 from Same-Slide Spatial Multiomics Integration with IN-DEPTH Reveals Tumor Virus–Linked Spatial Reorganization of the Tumor Microenvironment

Stephanie Pei Tung Yiu, Yuzhou Chang, Yao Yu Yeo, Huaying Qiu et autres

Details of batch effect correction for the DLBCL IN-DEPTH datasets.

Supp Fig 10 from Same-Slide Spatial Multiomics Integration with IN-DEPTH Reveals Tumor Virus–Linked Spatial Reorganization of the Tumor Microenvironment

Stephanie Pei Tung Yiu, Yuzhou Chang, Yao Yu Yeo, Huaying Qiu et autres

Additional supporting data for the ligand-receptor analysis.

Supp Fig 5 from Same-Slide Spatial Multiomics Integration with IN-DEPTH Reveals Tumor Virus–Linked Spatial Reorganization of the Tumor Microenvironment

Stephanie Pei Tung Yiu, Yuzhou Chang, Yao Yu Yeo, Huaying Qiu et autres

Additional antibody staining specificity validation and cell phenotyping maps across DLBCL tissue sections.

Supp Fig 6 from Same-Slide Spatial Multiomics Integration with IN-DEPTH Reveals Tumor Virus–Linked Spatial Reorganization of the Tumor Microenvironment

Stephanie Pei Tung Yiu, Yuzhou Chang, Yao Yu Yeo, Huaying Qiu et autres

Additional details on the CODEX-GeoMx spatial alignment, integration workflow, and batch effect correction for the DLBCL cohort.

Supp Table 7 from Same-Slide Spatial Multiomics Integration with IN-DEPTH Reveals Tumor Virus–Linked Spatial Reorganization of the Tumor Microenvironment

Stephanie Pei Tung Yiu, Yuzhou Chang, Yao Yu Yeo, Huaying Qiu et autres

GSVA pathways identified in DLBCL datasets at multicellular and single-cell resolution using SGCC.

Supp Fig 4 from Same-Slide Spatial Multiomics Integration with IN-DEPTH Reveals Tumor Virus–Linked Spatial Reorganization of the Tumor Microenvironment

Stephanie Pei Tung Yiu, Yuzhou Chang, Yao Yu Yeo, Huaying Qiu et autres

Additional validation and parameter optimization of the SGCC method, including simulation benchmarking against classical spatial statistical methods and robustness testing across parameter settings.