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adata.X – Normalized, log1p-transformed gene expression matrix (float32, sparse). Cells were normalized using scran normalization followed by log1p transformation. Row index (adata.obs.index): cell barcodes in the format {barcode}_{sample_name}. Column index (adata.var.index): HGNC gene symbols (19,588 genes). adata.layers["counts"] – Raw UMI count matrix (integer-valued, float32, sparse) prior to normalization. Recommended for differential expression analysis or re-normalization workflows. adata.obsm["X_gex"] – 10-dimensional GEX latent embedding (float32, dense; 50,633 × 10) used for neighborhood graph construction and clustering. adata.obsm["X_umap"] – 2D UMAP coordinates (float32, dense; 50,633 × 2) computed from X_gex for visualization. adata.obs contains the following per-cell metadata: tcr: Unique TCR identifier constructed by concatenating IR_VJ_1_junction_aa, IR_VDJ_1_junction_aa, IR_VJ_1_v_call, IR_VJ_1_j_call, IR_VDJ_1_v_call, IR_VDJ_1_j_call, and individual (hyphen-delimited). Cells without a paired TCR are NaN. IR_VJ_1_junction_aa: TCR α-chain CDR3 amino acid sequence (IMGT junction definition). IR_VDJ_1_junction_aa: TCR β-chain CDR3 amino acid sequence (IMGT junction definition). IR_VJ_1_junction: TCR α-chain CDR3 nucleotide sequence. IR_VDJ_1_junction: TCR β-chain CDR3 nucleotide sequence. IR_VJ_1_v_call / IR_VJ_1_j_call: TCR α-chain V and J gene segments (IMGT nomenclature). IR_VDJ_1_v_call / IR_VDJ_1_j_call: TCR β-chain V and J gene segments (IMGT nomenclature). sample_name: Sample identifier (format: {PatientID}-{treat}-{tissue}, e.g. "31-POST-TUMOR"). individual: Patient ID used in TCR construction (POST-#1 to POST-#8; PRE-#1 to PRE-#4). treat: Treatment timepoint. PRE: pre-CRT biopsy; POST: post-CRT surgical specimen. response: Pathological response to chemoradiotherapy. pCR: complete response (ypT0N0); non-pCR: residual disease; PRE: pre-treatment (no response assigned). tissue: Tissue compartment of origin (Tumor / LymphNode). leiden2CD8celltype2: CD8⁺ T cell subtype annotation. Tn: naïve; Tpex: precursor exhausted; Trm-like: tissue-resident memory-like; Tem.str: effector memory stem-like; Tex.trans1/Tex.trans2: transitional exhausted; Tex.eff: effector-like exhausted; Tex.str: stem-like exhausted; Tex.term/IEL: terminally exhausted/intraepithelial lymphocyte-like. Naïve, Cytotoxicity, Exhaustion, TCR Signaling, Cytokine/Cytokine receptor, Chemokine/Chemokine receptor, IFN Response, Anergy, Stress response: Per-cell functional gene signature scores (float64, z-scored across all cells).