10x Genomics sample-multiplexed single-cell RNA-seq dataset of paired blood and intra-tumoral T cells from melanoma patients

This dataset contains 10x Genomics sample-multiplexed single-cell RNA sequencing (scRNA-seq) data from paired peripheral blood mononuclear cells (PBMC) and tumor-infiltrating lymph node (TILN) samples of nine melanoma patients. Ex vivo single-cell transcriptomic profiling was performed on tumor antigen-specific CD4 T cells (NY-ESO-1_87–99, NY-ESO-1_123–137, MAGE-A3_243–258), pathogen-specific CD4 T cells (HA_307–319, TT_947–960), as well as bulk CD4 and CD8 T cells isolated from paired blood and tumor samples. Antigen-specific T cells were identified and sorted using fluorescent peptide–MHC class II multimers. In total, 21,806 single T cells were sequenced. Prior to single-cell capture, samples were stained with peptide–MHC class II multimers and antibodies against CD3, CD4, and CD8, followed by hashing using TotalSeq-C oligonucleotide-conjugated antibodies to enable sample multiplexing and demultiplexing. Sorted viable T cells were processed using the Chromium Next GEM Single Cell 5′ Kit v2 and 5′ Feature Barcode technology (10x Genomics). Libraries were sequenced on an Illumina NovaSeq 6000 platform (paired-end 28 × 90 bp). The dataset includes: Gene expression count matrices generated using the 10x Genomics platform Feature barcode (hashtag) information used for sample multiplexing Metadata linking each cell to patient, tissue origin (PBMC or TILN), antigen specificity (including tetramer-positive populations), and sample type The accompanying metadata.xlsx file contains detailed sample annotations and hashtag assignments used for demultiplexing individual patients and sample types.