Low T cell diversity is associated with poor outcome in bladder cancer - Single cell RNAseq and TCRseq data

T cells are crucial effector cells in the endogenous defense against cancer, yet the clinical impact of their quantity, diversity, and dynamics remains underexplored. In this study we performed single cell RNAseq paired with single cell TCR-seq on tumor and blood samples from 4 patients (n samples = 8). The goal was to investigate T cell subtypes of expanded and non-expanded T cell clones in blood and in tumors.

Type: Transcriptome Sequencing
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 1 Publication

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD50000001381	For this dataset we performed single cell RNAseq paired with single cell TCR-seq on tumor and blood samples from 4 patients. This dataset contains 4 tumor samples as well as 4 blood samples. Each sample is made up of 2 sets of paired fastq files. The first pair contains reads corresponding to RNA transcripts (_Transcripts in file name), while the second pair contain reads corresponding to TCRs (_VDJ in file name). Sequenced on the Illumina NovaSeq6000 platform in a paired-end run using an SP flow cell (v1.5, 300 cycles).	Illumina NovaSeq 6000	8

Publications	Citations
Low T cell diversity associates with poor outcome in bladder cancer: A comprehensive longitudinal analysis of the T cell receptor repertoire. Kjær A, Kristjánsdóttir N, Juul RI, Nordentoft I, Birkenkamp-Demtröder K, Ahrenfeldt J, Strandgaard T, Radif D, Hodgson D, Abbosh C, Aerts HJWL, Agerbæk M, Jensen JB, Birkbak NJ, Dyrskjøt L. Cell Rep Med 6: 2025 102101	2