Single-cell transcriptome and TCR repertoire of PD-1 fate-mapped immune cells during cyclophosphamide and PD-1 blockade in syngeneic subcutaneous LLC tumor allografts

We profiled PD-1–expressing immune populations during therapy using a tamoxifen-inducible Pdcd1-CreERT2 fate-mapping mouse crossed to a Rosa26 reporter. Single-cell RNA-seq (BD Rhapsody whole-transcriptome; paired-end Illumina), targeted VDJ-TCR libraries, and sample-tag libraries were generated from syngeneic subcutaneous Lewis lung carcinoma (LLC) allografts and draining lymph nodes of mice treated with cyclophosphamide (CTX), anti-PD-1, the CTX+anti-PD-1 combination, or isotype controls. This submission provides raw FASTQ files for transcriptome, TCR, and sample-tag libraries with associated BioSample metadata. The dataset enables reconstruction of the tumor immune landscape with a focus on PD-1 lineage cells, quantification of progenitor-exhausted CD8 T-cell states (e.g., SLAMF6? CD69?), and clonotype tracking across treatments. In brief, combination therapy increased the frequency of those progenitor-exhausted CD8 T cells and uniquely expanded TCR clonotypes among PD-1 fate-mapped cells. Species: Mus musculus; assays: scRNA-seq and scTCR-seq. Processed count matrices may be released separately.