Single-Cell Analysis study with RNA-Seq, RNA Seq (NGS) data on dbGaP (29 participants)

phs002289 — Yale SPORE in Skin Cancer Project 2

Understanding the relationship between tumor and peripheral immune environments could allow longitudinal immune monitoring in cancer. Here, we examined whether T cells that share the same TCRab and are found in both tumor and blood can be interrogated to gain insight into the ongoing tumor T cell response. Paired transcriptome and TCRab repertoire of circulating and tumor-infiltrating T cells were analyzed at the single cell level from matched tumor and blood from patients with metastatic melanoma. The data shared here consist of gene expression matrix and fastq files obtained from sequencing single-cell libraries generated with the Chromium (TM) 5' technique. For each of 18 immunotherapy naive and 11 previously treated melanoma patients, T cells (Live/<a href="https://www.ncbi.nlm.nih.gov/gene/5788">CD45</a>+/TcRab+) were FACS-sorted from PBMCs and freshly resected tumors. Metadata associated with each individual cell consist of Patient I.D., biological sex, immunotherapy status, amino acid and nucleotide CDR3 sequence of the TCR alpha and beta chain (obtained from matched VDJ region enriched libraries), and sequencing batch. Further details about previous treatment history and other clinical parameters can be found in the associated manuscripts (Lucca et al., 2021: PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/33651881/">33651881</a>; Lu et al., PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/39609626/">39609626</a>).